add complicated test case for BubbleMerge
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/EdgeListWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/EdgeListWritable.java
index 97f34f9..3dfeef4 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/EdgeListWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/EdgeListWritable.java
@@ -76,6 +76,12 @@
return edges.add(new EdgeWritable(element));
}
+ public boolean add(VKmerBytesWritable kmer) {
+ EdgeWritable edge = new EdgeWritable();
+ edge.setKey(kmer);
+ return edges.add(edge);
+ }
+
public EdgeWritable set(int i, EdgeWritable element) {
return edges.set(i, element);
}
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java
index e8fb93f..6cfbb2e 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java
@@ -354,6 +354,11 @@
internalKmer.mergeWithKmerInDir(dir, KmerBytesWritable.lettersInKmer, other.internalKmer);
}
+ public void addWithNode(final NodeWritable other){
+ addEdges(other);
+ addCoverage(other);
+ }
+
/**
* update my edge list
@@ -419,6 +424,12 @@
break;
}
}
+
+ public void addEdges(NodeWritable other){
+ for(byte dir : DirectionFlag.values){
+ edges[dir].unionUpdate(other.edges[dir]);
+ }
+ }
private void mergeStartAndEndReadIDs(byte dir, NodeWritable other) {
int K = KmerBytesWritable.lettersInKmer;
diff --git a/genomix/genomix-hadoop/data/webmap/BubbleMerge_TestSet/AdjFR/AdjFR b/genomix/genomix-hadoop/data/webmap/BubbleMerge_TestSet/AdjFR/AdjFR
new file mode 100644
index 0000000..d65597a
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/BubbleMerge_TestSet/AdjFR/AdjFR
@@ -0,0 +1,2 @@
+1 ACAT
+2 ATGA
diff --git a/genomix/genomix-hadoop/data/webmap/BubbleMerge_TestSet/FRandRF/invalid b/genomix/genomix-hadoop/data/webmap/BubbleMerge_TestSet/FRandRF/invalid
new file mode 100644
index 0000000..df1afab
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/BubbleMerge_TestSet/FRandRF/invalid
@@ -0,0 +1,2 @@
+1 CCTACGAT
+2 CCTCAGAT
diff --git a/genomix/genomix-hadoop/data/webmap/BubbleMerge_TestSet/InvalidBubble/invalid b/genomix/genomix-hadoop/data/webmap/BubbleMerge_TestSet/InvalidBubble/invalid
deleted file mode 100644
index 75d2dc2..0000000
--- a/genomix/genomix-hadoop/data/webmap/BubbleMerge_TestSet/InvalidBubble/invalid
+++ /dev/null
@@ -1,6 +0,0 @@
-1 CTTA
-2 AAGAA
-3 TTTC
-4 TAAC
-5 TTGTT
-6 CAAA
diff --git a/genomix/genomix-hadoop/data/webmap/BubbleMerge_TestSet/LtoL/LtoL b/genomix/genomix-hadoop/data/webmap/BubbleMerge_TestSet/LtoL/LtoL
index a5e5a0c..a12b242 100644
--- a/genomix/genomix-hadoop/data/webmap/BubbleMerge_TestSet/LtoL/LtoL
+++ b/genomix/genomix-hadoop/data/webmap/BubbleMerge_TestSet/LtoL/LtoL
@@ -1,2 +1,2 @@
-1 ACCGGGA
-2 ACCTGGA
+1 ACGAAAGGA
+2 ACGGCTGGA
diff --git a/genomix/genomix-hadoop/data/webmap/BubbleMerge_TestSet/LtoR/LtoR b/genomix/genomix-hadoop/data/webmap/BubbleMerge_TestSet/LtoR/LtoR
index 656e362..ce5ffe7 100644
--- a/genomix/genomix-hadoop/data/webmap/BubbleMerge_TestSet/LtoR/LtoR
+++ b/genomix/genomix-hadoop/data/webmap/BubbleMerge_TestSet/LtoR/LtoR
@@ -1,4 +1,2 @@
-1 GTAA
-3 TAACAAA
-4 TTTCTTA
-5 ATTT
+1 ACGAAAGGT
+2 ACGGCTGGT
diff --git a/genomix/genomix-hadoop/data/webmap/BubbleMerge_TestSet/RtoL/RtoL b/genomix/genomix-hadoop/data/webmap/BubbleMerge_TestSet/RtoL/RtoL
index cd520d9..37f13aa 100644
--- a/genomix/genomix-hadoop/data/webmap/BubbleMerge_TestSet/RtoL/RtoL
+++ b/genomix/genomix-hadoop/data/webmap/BubbleMerge_TestSet/RtoL/RtoL
@@ -1,4 +1,2 @@
-1 GTTA
-2 TAACAAA
-3 TTTCTTA
-4 AAAT
+1 GCGAAAGGA
+2 GCGGCTGGA
diff --git a/genomix/genomix-hadoop/data/webmap/BubbleMerge_TestSet/RtoR/RtoR b/genomix/genomix-hadoop/data/webmap/BubbleMerge_TestSet/RtoR/RtoR
index 4739d75..a05f988 100644
--- a/genomix/genomix-hadoop/data/webmap/BubbleMerge_TestSet/RtoR/RtoR
+++ b/genomix/genomix-hadoop/data/webmap/BubbleMerge_TestSet/RtoR/RtoR
@@ -1,4 +1,2 @@
-1 GTTA
-3 TAACAAA
-4 TTTCTTA
-5 TTTA
+1 GCGAAAGGT
+2 GCGGCTGGT
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTestSuite.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTestSuite.java
index 626f721..54ac300 100644
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTestSuite.java
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTestSuite.java
@@ -24,7 +24,8 @@
private static int SIZE_KMER = 3;
public static final String PreFix = "data/webmap/BubbleMerge_TestSet";
public static final String[] TestDir = { PreFix + File.separator
- + "LtoL"};
+ + "AdjFR"
+ };
// + "SimpleBubble", PreFix + File.separator
// + "LtoL", PreFix + File.separator
// + "LtoR", PreFix + File.separator
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleAdd/AdjFR/..binmerge.crc b/genomix/genomix-pregelix/data/TestSet/BubbleAdd/AdjFR/..binmerge.crc
new file mode 100644
index 0000000..0a16b5c
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleAdd/AdjFR/..binmerge.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleAdd/AdjFR/.binmerge b/genomix/genomix-pregelix/data/TestSet/BubbleAdd/AdjFR/.binmerge
new file mode 100755
index 0000000..216a373
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleAdd/AdjFR/.binmerge
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleAdd/AdjFR/bin/.part-00000.crc b/genomix/genomix-pregelix/data/TestSet/BubbleAdd/AdjFR/bin/.part-00000.crc
new file mode 100644
index 0000000..9ad6666
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleAdd/AdjFR/bin/.part-00000.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleAdd/AdjFR/bin/part-00000 b/genomix/genomix-pregelix/data/TestSet/BubbleAdd/AdjFR/bin/part-00000
new file mode 100755
index 0000000..dff0874
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleAdd/AdjFR/bin/part-00000
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleAdd/AdjFR/data b/genomix/genomix-pregelix/data/TestSet/BubbleAdd/AdjFR/data
new file mode 100644
index 0000000..3be6740
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleAdd/AdjFR/data
@@ -0,0 +1,3 @@
+ACA {[] [{ATG:[1]}] [] [] {5':[(1-0_0)], ~5':[]} 1.0x}
+TCA {[] [{ATG:[2]}] [] [] {5':[], ~5':[]} 1.0x}
+ATG {[] [{TCA:[2]}, {ACA:[1]}] [] [] {5':[(2-0_0)], ~5':[]} 2.0x}
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleAdd/AdjFR/graphviz/result.ps b/genomix/genomix-pregelix/data/TestSet/BubbleAdd/AdjFR/graphviz/result.ps
new file mode 100644
index 0000000..c3840de
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleAdd/AdjFR/graphviz/result.ps
@@ -0,0 +1,424 @@
+%!PS-Adobe-3.0
+%%Creator: graphviz version 2.26.3 (20100126.1600)
+%%Title: G
+%%Pages: (atend)
+%%BoundingBox: (atend)
+%%EndComments
+save
+%%BeginProlog
+/DotDict 200 dict def
+DotDict begin
+
+/setupLatin1 {
+mark
+/EncodingVector 256 array def
+ EncodingVector 0
+
+ISOLatin1Encoding 0 255 getinterval putinterval
+EncodingVector 45 /hyphen put
+
+% Set up ISO Latin 1 character encoding
+/starnetISO {
+ dup dup findfont dup length dict begin
+ { 1 index /FID ne { def }{ pop pop } ifelse
+ } forall
+ /Encoding EncodingVector def
+ currentdict end definefont
+} def
+/Times-Roman starnetISO def
+/Times-Italic starnetISO def
+/Times-Bold starnetISO def
+/Times-BoldItalic starnetISO def
+/Helvetica starnetISO def
+/Helvetica-Oblique starnetISO def
+/Helvetica-Bold starnetISO def
+/Helvetica-BoldOblique starnetISO def
+/Courier starnetISO def
+/Courier-Oblique starnetISO def
+/Courier-Bold starnetISO def
+/Courier-BoldOblique starnetISO def
+cleartomark
+} bind def
+
+%%BeginResource: procset graphviz 0 0
+/coord-font-family /Times-Roman def
+/default-font-family /Times-Roman def
+/coordfont coord-font-family findfont 8 scalefont def
+
+/InvScaleFactor 1.0 def
+/set_scale {
+ dup 1 exch div /InvScaleFactor exch def
+ scale
+} bind def
+
+% styles
+/solid { [] 0 setdash } bind def
+/dashed { [9 InvScaleFactor mul dup ] 0 setdash } bind def
+/dotted { [1 InvScaleFactor mul 6 InvScaleFactor mul] 0 setdash } bind def
+/invis {/fill {newpath} def /stroke {newpath} def /show {pop newpath} def} bind def
+/bold { 2 setlinewidth } bind def
+/filled { } bind def
+/unfilled { } bind def
+/rounded { } bind def
+/diagonals { } bind def
+
+% hooks for setting color
+/nodecolor { sethsbcolor } bind def
+/edgecolor { sethsbcolor } bind def
+/graphcolor { sethsbcolor } bind def
+/nopcolor {pop pop pop} bind def
+
+/beginpage { % i j npages
+ /npages exch def
+ /j exch def
+ /i exch def
+ /str 10 string def
+ npages 1 gt {
+ gsave
+ coordfont setfont
+ 0 0 moveto
+ (\() show i str cvs show (,) show j str cvs show (\)) show
+ grestore
+ } if
+} bind def
+
+/set_font {
+ findfont exch
+ scalefont setfont
+} def
+
+% draw text fitted to its expected width
+/alignedtext { % width text
+ /text exch def
+ /width exch def
+ gsave
+ width 0 gt {
+ [] 0 setdash
+ text stringwidth pop width exch sub text length div 0 text ashow
+ } if
+ grestore
+} def
+
+/boxprim { % xcorner ycorner xsize ysize
+ 4 2 roll
+ moveto
+ 2 copy
+ exch 0 rlineto
+ 0 exch rlineto
+ pop neg 0 rlineto
+ closepath
+} bind def
+
+/ellipse_path {
+ /ry exch def
+ /rx exch def
+ /y exch def
+ /x exch def
+ matrix currentmatrix
+ newpath
+ x y translate
+ rx ry scale
+ 0 0 1 0 360 arc
+ setmatrix
+} bind def
+
+/endpage { showpage } bind def
+/showpage { } def
+
+/layercolorseq
+ [ % layer color sequence - darkest to lightest
+ [0 0 0]
+ [.2 .8 .8]
+ [.4 .8 .8]
+ [.6 .8 .8]
+ [.8 .8 .8]
+ ]
+def
+
+/layerlen layercolorseq length def
+
+/setlayer {/maxlayer exch def /curlayer exch def
+ layercolorseq curlayer 1 sub layerlen mod get
+ aload pop sethsbcolor
+ /nodecolor {nopcolor} def
+ /edgecolor {nopcolor} def
+ /graphcolor {nopcolor} def
+} bind def
+
+/onlayer { curlayer ne {invis} if } def
+
+/onlayers {
+ /myupper exch def
+ /mylower exch def
+ curlayer mylower lt
+ curlayer myupper gt
+ or
+ {invis} if
+} def
+
+/curlayer 0 def
+
+%%EndResource
+%%EndProlog
+%%BeginSetup
+14 default-font-family set_font
+1 setmiterlimit
+% /arrowlength 10 def
+% /arrowwidth 5 def
+
+% make sure pdfmark is harmless for PS-interpreters other than Distiller
+/pdfmark where {pop} {userdict /pdfmark /cleartomark load put} ifelse
+% make '<<' and '>>' safe on PS Level 1 devices
+/languagelevel where {pop languagelevel}{1} ifelse
+2 lt {
+ userdict (<<) cvn ([) cvn load put
+ userdict (>>) cvn ([) cvn load put
+} if
+
+%%EndSetup
+setupLatin1
+%%Page: 1 1
+%%PageBoundingBox: 36 36 376 148
+%%PageOrientation: Portrait
+0 0 1 beginpage
+gsave
+36 36 340 112 boxprim clip newpath
+1 1 set_scale 0 rotate 40 41 translate
+% ACA
+gsave
+0 0 0.75294 nodecolor
+newpath 0 0 moveto
+0 104 lineto
+56 104 lineto
+56 0 lineto
+closepath fill
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 0 0 moveto
+0 104 lineto
+56 104 lineto
+56 0 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+13 87.4 moveto 30 (ACA) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 0 78 moveto
+56 78 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+9.5 61.4 moveto 37 (5':[1]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 0 52 moveto
+56 52 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+8 35.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 0 26 moveto
+56 26 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+16.5 9.4 moveto 23 (1.0) alignedtext
+grestore
+% ATG
+gsave
+0 0 0.75294 nodecolor
+newpath 138 0 moveto
+138 104 lineto
+194 104 lineto
+194 0 lineto
+closepath fill
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 138 0 moveto
+138 104 lineto
+194 104 lineto
+194 0 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+151 87.4 moveto 30 (ATG) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 138 78 moveto
+194 78 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+147.5 61.4 moveto 37 (5':[2]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 138 52 moveto
+194 52 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+146 35.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 138 26 moveto
+194 26 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+154.5 9.4 moveto 23 (2.0) alignedtext
+grestore
+% ACA->ATG
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 56.26 52 moveto
+76.82 52 104.89 52 127.5 52 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 127.78 55.5 moveto
+137.78 52 lineto
+127.78 48.5 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 127.78 55.5 moveto
+137.78 52 lineto
+127.78 48.5 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+74 57.4 moveto 46 (FR: [1]) alignedtext
+grestore
+% ATG->ACA
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 137.51 35.99 moveto
+131.87 33.51 125.87 31.33 120 30 curveto
+100.06 25.48 93.94 25.48 74 30 curveto
+71.34 30.6 68.65 31.38 65.99 32.28 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 64.53 29.09 moveto
+56.49 35.99 lineto
+67.08 35.61 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 64.53 29.09 moveto
+56.49 35.99 lineto
+67.08 35.61 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+74 35.4 moveto 46 (FR: [1]) alignedtext
+grestore
+% TCA
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 276 0 moveto
+276 104 lineto
+332 104 lineto
+332 0 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+290 87.4 moveto 28 (TCA) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 276 78 moveto
+332 78 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+290 61.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 276 52 moveto
+332 52 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+284 35.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 276 26 moveto
+332 26 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+292.5 9.4 moveto 23 (1.0) alignedtext
+grestore
+% ATG->TCA
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 194.26 52 moveto
+214.82 52 242.89 52 265.5 52 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 265.78 55.5 moveto
+275.78 52 lineto
+265.78 48.5 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 265.78 55.5 moveto
+275.78 52 lineto
+265.78 48.5 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+212 57.4 moveto 46 (FR: [2]) alignedtext
+grestore
+% TCA->ATG
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 275.83 38.35 moveto
+270.06 36.13 263.93 34.18 258 33 curveto
+237.95 29.02 232.05 29.02 212 33 curveto
+209.31 33.53 206.58 34.23 203.87 35.03 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 202.5 31.8 moveto
+194.17 38.35 lineto
+204.76 38.42 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 202.5 31.8 moveto
+194.17 38.35 lineto
+204.76 38.42 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+212 38.4 moveto 46 (FR: [2]) alignedtext
+grestore
+endpage
+showpage
+grestore
+%%PageTrailer
+%%EndPage: 1
+%%Trailer
+%%Pages: 1
+%%BoundingBox: 36 36 376 148
+end
+restore
+%%EOF
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/.txt.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/.txt.crc
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/.txt.crc
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/.part-0.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/.part-0.crc
new file mode 100644
index 0000000..97e2b9f
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/.part-0.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/.part-1.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/.part-1.crc
new file mode 100644
index 0000000..dfee1e4
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/.part-1.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/.part-2.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/.part-2.crc
new file mode 100644
index 0000000..24f7061
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/.part-2.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/.part-3.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/.part-3.crc
new file mode 100644
index 0000000..095692e
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/.part-3.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/.part-4.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/.part-4.crc
new file mode 100644
index 0000000..c329050
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/.part-4.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/.part-5.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/.part-5.crc
new file mode 100644
index 0000000..4151ca0
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/.part-5.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/.part-6.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/.part-6.crc
new file mode 100644
index 0000000..c67529c
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/.part-6.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/.part-7.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/.part-7.crc
new file mode 100644
index 0000000..1889d80
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/.part-7.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/part-0 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/part-0
new file mode 100755
index 0000000..83bfb42
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/part-0
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/part-1 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/part-1
new file mode 100755
index 0000000..2a3d766
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/part-1
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/part-2 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/part-2
new file mode 100755
index 0000000..e7b6ad0
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/part-2
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/part-3 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/part-3
new file mode 100755
index 0000000..6bf56e9
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/part-3
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/part-4 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/part-4
new file mode 100755
index 0000000..07e31ce
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/part-4
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/part-5 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/part-5
new file mode 100755
index 0000000..a1f35ce
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/part-5
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/part-6 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/part-6
new file mode 100755
index 0000000..83c4642
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/part-6
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/part-7 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/part-7
new file mode 100755
index 0000000..bf2e129
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/bin/part-7
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/graphviz/result.ps b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/graphviz/result.ps
new file mode 100644
index 0000000..583b350
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/graphviz/result.ps
@@ -0,0 +1,767 @@
+%!PS-Adobe-3.0
+%%Creator: graphviz version 2.26.3 (20100126.1600)
+%%Title: G
+%%Pages: (atend)
+%%BoundingBox: (atend)
+%%EndComments
+save
+%%BeginProlog
+/DotDict 200 dict def
+DotDict begin
+
+/setupLatin1 {
+mark
+/EncodingVector 256 array def
+ EncodingVector 0
+
+ISOLatin1Encoding 0 255 getinterval putinterval
+EncodingVector 45 /hyphen put
+
+% Set up ISO Latin 1 character encoding
+/starnetISO {
+ dup dup findfont dup length dict begin
+ { 1 index /FID ne { def }{ pop pop } ifelse
+ } forall
+ /Encoding EncodingVector def
+ currentdict end definefont
+} def
+/Times-Roman starnetISO def
+/Times-Italic starnetISO def
+/Times-Bold starnetISO def
+/Times-BoldItalic starnetISO def
+/Helvetica starnetISO def
+/Helvetica-Oblique starnetISO def
+/Helvetica-Bold starnetISO def
+/Helvetica-BoldOblique starnetISO def
+/Courier starnetISO def
+/Courier-Oblique starnetISO def
+/Courier-Bold starnetISO def
+/Courier-BoldOblique starnetISO def
+cleartomark
+} bind def
+
+%%BeginResource: procset graphviz 0 0
+/coord-font-family /Times-Roman def
+/default-font-family /Times-Roman def
+/coordfont coord-font-family findfont 8 scalefont def
+
+/InvScaleFactor 1.0 def
+/set_scale {
+ dup 1 exch div /InvScaleFactor exch def
+ scale
+} bind def
+
+% styles
+/solid { [] 0 setdash } bind def
+/dashed { [9 InvScaleFactor mul dup ] 0 setdash } bind def
+/dotted { [1 InvScaleFactor mul 6 InvScaleFactor mul] 0 setdash } bind def
+/invis {/fill {newpath} def /stroke {newpath} def /show {pop newpath} def} bind def
+/bold { 2 setlinewidth } bind def
+/filled { } bind def
+/unfilled { } bind def
+/rounded { } bind def
+/diagonals { } bind def
+
+% hooks for setting color
+/nodecolor { sethsbcolor } bind def
+/edgecolor { sethsbcolor } bind def
+/graphcolor { sethsbcolor } bind def
+/nopcolor {pop pop pop} bind def
+
+/beginpage { % i j npages
+ /npages exch def
+ /j exch def
+ /i exch def
+ /str 10 string def
+ npages 1 gt {
+ gsave
+ coordfont setfont
+ 0 0 moveto
+ (\() show i str cvs show (,) show j str cvs show (\)) show
+ grestore
+ } if
+} bind def
+
+/set_font {
+ findfont exch
+ scalefont setfont
+} def
+
+% draw text fitted to its expected width
+/alignedtext { % width text
+ /text exch def
+ /width exch def
+ gsave
+ width 0 gt {
+ [] 0 setdash
+ text stringwidth pop width exch sub text length div 0 text ashow
+ } if
+ grestore
+} def
+
+/boxprim { % xcorner ycorner xsize ysize
+ 4 2 roll
+ moveto
+ 2 copy
+ exch 0 rlineto
+ 0 exch rlineto
+ pop neg 0 rlineto
+ closepath
+} bind def
+
+/ellipse_path {
+ /ry exch def
+ /rx exch def
+ /y exch def
+ /x exch def
+ matrix currentmatrix
+ newpath
+ x y translate
+ rx ry scale
+ 0 0 1 0 360 arc
+ setmatrix
+} bind def
+
+/endpage { showpage } bind def
+/showpage { } def
+
+/layercolorseq
+ [ % layer color sequence - darkest to lightest
+ [0 0 0]
+ [.2 .8 .8]
+ [.4 .8 .8]
+ [.6 .8 .8]
+ [.8 .8 .8]
+ ]
+def
+
+/layerlen layercolorseq length def
+
+/setlayer {/maxlayer exch def /curlayer exch def
+ layercolorseq curlayer 1 sub layerlen mod get
+ aload pop sethsbcolor
+ /nodecolor {nopcolor} def
+ /edgecolor {nopcolor} def
+ /graphcolor {nopcolor} def
+} bind def
+
+/onlayer { curlayer ne {invis} if } def
+
+/onlayers {
+ /myupper exch def
+ /mylower exch def
+ curlayer mylower lt
+ curlayer myupper gt
+ or
+ {invis} if
+} def
+
+/curlayer 0 def
+
+%%EndResource
+%%EndProlog
+%%BeginSetup
+14 default-font-family set_font
+1 setmiterlimit
+% /arrowlength 10 def
+% /arrowwidth 5 def
+
+% make sure pdfmark is harmless for PS-interpreters other than Distiller
+/pdfmark where {pop} {userdict /pdfmark /cleartomark load put} ifelse
+% make '<<' and '>>' safe on PS Level 1 devices
+/languagelevel where {pop languagelevel}{1} ifelse
+2 lt {
+ userdict (<<) cvn ([) cvn load put
+ userdict (>>) cvn ([) cvn load put
+} if
+
+%%EndSetup
+setupLatin1
+%%Page: 1 1
+%%PageBoundingBox: 36 36 748 396
+%%PageOrientation: Portrait
+0 0 1 beginpage
+gsave
+36 36 712 360 boxprim clip newpath
+1 1 set_scale 0 rotate 40 41 translate
+% TAA
+gsave
+0 0 0.75294 nodecolor
+newpath .5 0 moveto
+.5 130 lineto
+93.5 130 lineto
+93.5 0 lineto
+closepath fill
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath .5 0 moveto
+.5 130 lineto
+93.5 130 lineto
+93.5 0 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+32.5 113.4 moveto 29 (TAA) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath .5 104 moveto
+93.5 104 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+8.5 87.4 moveto 77 (5':[2,3,4,1]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath .5 78 moveto
+93.5 78 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+27 61.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath .5 52 moveto
+93.5 52 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+35.5 35.4 moveto 23 (4.0) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath .5 26 moveto
+93.5 26 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+32.5 9.4 moveto 29 (TAA) alignedtext
+grestore
+% AGC
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 192 82 moveto
+192 212 lineto
+260 212 lineto
+260 82 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+210.5 195.4 moveto 31 (AGC) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 192 186 moveto
+260 186 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+212 169.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 192 160 moveto
+260 160 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+206 143.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 192 134 moveto
+260 134 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+214.5 117.4 moveto 23 (2.0) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 192 108 moveto
+260 108 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+200 91.4 moveto 52 (AAGCC) alignedtext
+grestore
+% TAA->AGC
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 93.52 96.03 moveto
+99.63 99.59 105.88 103.02 112 106 curveto
+134.46 116.96 160.62 126.58 182.22 133.74 curveto
+stroke
+0 0 0 edgecolor
+newpath 181.2 137.09 moveto
+191.79 136.85 lineto
+183.36 130.43 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 181.2 137.09 moveto
+191.79 136.85 lineto
+183.36 130.43 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+114 135.4 moveto 58 (FF: [2,4]) alignedtext
+grestore
+% CCC
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 498 39 moveto
+498 169 lineto
+564 169 lineto
+564 39 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+516 152.4 moveto 30 (CCC) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 498 143 moveto
+564 143 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+517 126.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 498 117 moveto
+564 117 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+511 100.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 498 91 moveto
+564 91 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+519.5 74.4 moveto 23 (2.0) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 498 65 moveto
+564 65 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+506 48.4 moveto 50 (AACCC) alignedtext
+grestore
+% TAA->CCC
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 93.77 60 moveto
+163.93 53.62 300.32 45.58 414 65 curveto
+439.26 69.31 466.47 78.12 488.29 86.27 curveto
+stroke
+0 0 0 edgecolor
+newpath 487.32 89.65 moveto
+497.91 89.95 lineto
+489.82 83.11 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 487.32 89.65 moveto
+497.91 89.95 lineto
+489.82 83.11 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+280 60.4 moveto 58 (FF: [1,3]) alignedtext
+grestore
+% AGC->TAA
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 191.79 97.66 moveto
+186.38 92.38 180.42 87.63 174 84 curveto
+152.87 72.05 126.74 66.83 103.68 64.77 curveto
+stroke
+0 1 1 edgecolor
+newpath 103.9 61.28 moveto
+93.68 64.06 lineto
+103.4 68.26 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 103.9 61.28 moveto
+93.68 64.06 lineto
+103.4 68.26 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+112.5 89.4 moveto 61 (RR: [2,4]) alignedtext
+grestore
+% CCG
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 358 222 moveto
+358 352 lineto
+414 352 lineto
+414 222 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+370.5 335.4 moveto 31 (CCG) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 358 326 moveto
+414 326 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+372 309.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 358 300 moveto
+414 300 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+366 283.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 358 274 moveto
+414 274 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+374.5 257.4 moveto 23 (2.0) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 358 248 moveto
+414 248 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+370.5 231.4 moveto 31 (CCG) alignedtext
+grestore
+% AGC->CCG
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 246.27 212.23 moveto
+253.98 228.41 264.32 244.42 278 256 curveto
+297.49 272.51 325.3 280.24 347.82 283.85 curveto
+stroke
+0 0 0 edgecolor
+newpath 347.35 287.32 moveto
+357.74 285.24 lineto
+348.32 280.39 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 347.35 287.32 moveto
+357.74 285.24 lineto
+348.32 280.39 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+286.5 287.4 moveto 45 (FF: [2]) alignedtext
+grestore
+% AGG
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 358 74 moveto
+358 204 lineto
+414 204 lineto
+414 74 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+369.5 187.4 moveto 33 (AGG) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 358 178 moveto
+414 178 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+372 161.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 358 152 moveto
+414 152 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+366 135.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 358 126 moveto
+414 126 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+374.5 109.4 moveto 23 (1.0) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 358 100 moveto
+414 100 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+369.5 83.4 moveto 33 (AGG) alignedtext
+grestore
+% AGC->AGG
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 260.32 145.28 moveto
+286.02 144 321.17 142.24 347.77 140.91 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 348.05 144.4 moveto
+357.86 140.41 lineto
+347.7 137.41 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 348.05 144.4 moveto
+357.86 140.41 lineto
+347.7 137.41 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+286 149.4 moveto 46 (FR: [4]) alignedtext
+grestore
+% CCC->TAA
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 497.79 74.71 moveto
+492.12 70.68 486.08 66.93 480 64 curveto
+422.39 36.29 403.5 38.38 340 31 curveto
+257.77 21.44 162.57 37.51 103.56 50.65 curveto
+stroke
+0 1 1 edgecolor
+newpath 102.66 47.27 moveto
+93.69 52.9 lineto
+104.21 54.09 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 102.66 47.27 moveto
+93.69 52.9 lineto
+104.21 54.09 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+278.5 36.4 moveto 61 (RR: [1,3]) alignedtext
+grestore
+% CCA
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 648 39 moveto
+648 169 lineto
+704 169 lineto
+704 39 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+661 152.4 moveto 30 (CCA) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 648 143 moveto
+704 143 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+662 126.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 648 117 moveto
+704 117 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+656 100.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 648 91 moveto
+704 91 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+664.5 74.4 moveto 23 (1.0) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 648 65 moveto
+704 65 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+661 48.4 moveto 30 (CCA) alignedtext
+grestore
+% CCC->CCA
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 564.27 104 moveto
+586.16 104 614.89 104 637.74 104 curveto
+stroke
+0 0 0 edgecolor
+newpath 637.77 107.5 moveto
+647.77 104 lineto
+637.77 100.5 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 637.77 107.5 moveto
+647.77 104 lineto
+637.77 100.5 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+583.5 109.4 moveto 45 (FF: [3]) alignedtext
+grestore
+% CCC->CCG
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 497.97 133.45 moveto
+477.55 152.63 451.59 178.87 432 205 curveto
+427.69 210.75 423.51 216.94 419.53 223.26 curveto
+stroke
+0 0 0 edgecolor
+newpath 416.46 221.56 moveto
+414.24 231.92 lineto
+422.44 225.21 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 416.46 221.56 moveto
+414.24 231.92 lineto
+422.44 225.21 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+433.5 210.4 moveto 45 (FF: [1]) alignedtext
+grestore
+% CCA->CCC
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 647.83 90.35 moveto
+642.06 88.13 635.93 86.18 630 85 curveto
+609.07 80.85 603 81.22 582 85 curveto
+579.35 85.48 576.65 86.09 573.95 86.79 curveto
+stroke
+0 1 1 edgecolor
+newpath 572.84 83.47 moveto
+564.27 89.69 lineto
+574.85 90.17 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 572.84 83.47 moveto
+564.27 89.69 lineto
+574.85 90.17 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+582 90.4 moveto 48 (RR: [3]) alignedtext
+grestore
+% CCG->AGC
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 357.94 255.76 moveto
+352.16 249.71 346 243.54 340 238 curveto
+317.31 217.06 290.37 195.42 268.38 178.51 curveto
+stroke
+0 1 1 edgecolor
+newpath 270.29 175.56 moveto
+260.22 172.26 lineto
+266.04 181.12 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 270.29 175.56 moveto
+260.22 172.26 lineto
+266.04 181.12 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+278.5 243.4 moveto 61 (RR: [2,4]) alignedtext
+grestore
+% CCG->CCC
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 414.28 273.34 moveto
+434.82 262.21 462.05 244.79 480 223 curveto
+490.81 209.87 499.69 194.11 506.82 178.42 curveto
+stroke
+0 1 1 edgecolor
+newpath 510.05 179.78 moveto
+510.83 169.21 lineto
+503.63 176.99 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 510.05 179.78 moveto
+510.83 169.21 lineto
+503.63 176.99 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+432 267.4 moveto 48 (RR: [1]) alignedtext
+grestore
+% AGG->AGC
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 357.89 124.63 moveto
+352.11 122.3 345.97 120.24 340 119 curveto
+313.02 113.39 304.72 112.26 278 119 curveto
+275.2 119.7 272.39 120.59 269.61 121.62 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 268.14 118.44 moveto
+260.28 125.54 lineto
+270.85 124.89 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 268.14 118.44 moveto
+260.28 125.54 lineto
+270.85 124.89 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+279 124.4 moveto 60 (FR: [2,4]) alignedtext
+grestore
+endpage
+showpage
+grestore
+%%PageTrailer
+%%EndPage: 1
+%%Trailer
+%%Pages: 1
+%%BoundingBox: 36 36 748 396
+end
+restore
+%%EOF
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/txt b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/txt
new file mode 100755
index 0000000..0e9a51c
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/BubbleWithTip/txt
@@ -0,0 +1,6 @@
+TAA {[{AGC:[2,4]}, {CCC:[1,3]}] [] [] [] {5':[(2-0_0),(3-0_0),(4-0_0),(1-0_0)], ~5':[]}TAA 4.0x}
+CCA {[] [] [] [{CCC:[3]}] {5':[], ~5':[]}CCA 1.0x}
+CCC {[{CCG:[1]}, {CCA:[3]}] [] [] [{TAA:[1,3]}] {5':[], ~5':[]}AACCC 2.0x}
+CCG {[] [] [] [{AGC:[2,4]}, {CCC:[1]}] {5':[], ~5':[]}CCG 2.0x}
+AGC {[{CCG:[2]}] [{AGG:[4]}] [] [{TAA:[2,4]}] {5':[], ~5':[]}AAGCC 2.0x}
+AGG {[] [{AGC:[2,4]}] [] [] {5':[], ~5':[]}AGG 1.0x}
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/.txt.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/.txt.crc
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/.txt.crc
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/.part-0.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/.part-0.crc
new file mode 100644
index 0000000..00a8fd9
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/.part-0.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/.part-1.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/.part-1.crc
new file mode 100644
index 0000000..756dfa0
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/.part-1.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/.part-2.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/.part-2.crc
new file mode 100644
index 0000000..88a3370
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/.part-2.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/.part-3.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/.part-3.crc
new file mode 100644
index 0000000..6daf13f
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/.part-3.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/.part-4.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/.part-4.crc
new file mode 100644
index 0000000..d19f93d
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/.part-4.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/.part-5.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/.part-5.crc
new file mode 100644
index 0000000..562629c
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/.part-5.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/.part-6.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/.part-6.crc
new file mode 100644
index 0000000..3a57cae
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/.part-6.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/.part-7.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/.part-7.crc
new file mode 100644
index 0000000..f999b38
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/.part-7.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/part-0 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/part-0
new file mode 100755
index 0000000..7a1f06e
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/part-0
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/part-1 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/part-1
new file mode 100755
index 0000000..d4c5f69
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/part-1
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/part-2 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/part-2
new file mode 100755
index 0000000..0155c18
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/part-2
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/part-3 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/part-3
new file mode 100755
index 0000000..18aa9e7
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/part-3
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/part-4 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/part-4
new file mode 100755
index 0000000..6e3ed62
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/part-4
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/part-5 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/part-5
new file mode 100755
index 0000000..a598b3d
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/part-5
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/part-6 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/part-6
new file mode 100755
index 0000000..f4de65c
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/part-6
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/part-7 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/part-7
new file mode 100755
index 0000000..de06337
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/bin/part-7
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/graphviz/result.ps b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/graphviz/result.ps
new file mode 100644
index 0000000..ecd12a7
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/graphviz/result.ps
@@ -0,0 +1,580 @@
+%!PS-Adobe-3.0
+%%Creator: graphviz version 2.26.3 (20100126.1600)
+%%Title: G
+%%Pages: (atend)
+%%BoundingBox: (atend)
+%%EndComments
+save
+%%BeginProlog
+/DotDict 200 dict def
+DotDict begin
+
+/setupLatin1 {
+mark
+/EncodingVector 256 array def
+ EncodingVector 0
+
+ISOLatin1Encoding 0 255 getinterval putinterval
+EncodingVector 45 /hyphen put
+
+% Set up ISO Latin 1 character encoding
+/starnetISO {
+ dup dup findfont dup length dict begin
+ { 1 index /FID ne { def }{ pop pop } ifelse
+ } forall
+ /Encoding EncodingVector def
+ currentdict end definefont
+} def
+/Times-Roman starnetISO def
+/Times-Italic starnetISO def
+/Times-Bold starnetISO def
+/Times-BoldItalic starnetISO def
+/Helvetica starnetISO def
+/Helvetica-Oblique starnetISO def
+/Helvetica-Bold starnetISO def
+/Helvetica-BoldOblique starnetISO def
+/Courier starnetISO def
+/Courier-Oblique starnetISO def
+/Courier-Bold starnetISO def
+/Courier-BoldOblique starnetISO def
+cleartomark
+} bind def
+
+%%BeginResource: procset graphviz 0 0
+/coord-font-family /Times-Roman def
+/default-font-family /Times-Roman def
+/coordfont coord-font-family findfont 8 scalefont def
+
+/InvScaleFactor 1.0 def
+/set_scale {
+ dup 1 exch div /InvScaleFactor exch def
+ scale
+} bind def
+
+% styles
+/solid { [] 0 setdash } bind def
+/dashed { [9 InvScaleFactor mul dup ] 0 setdash } bind def
+/dotted { [1 InvScaleFactor mul 6 InvScaleFactor mul] 0 setdash } bind def
+/invis {/fill {newpath} def /stroke {newpath} def /show {pop newpath} def} bind def
+/bold { 2 setlinewidth } bind def
+/filled { } bind def
+/unfilled { } bind def
+/rounded { } bind def
+/diagonals { } bind def
+
+% hooks for setting color
+/nodecolor { sethsbcolor } bind def
+/edgecolor { sethsbcolor } bind def
+/graphcolor { sethsbcolor } bind def
+/nopcolor {pop pop pop} bind def
+
+/beginpage { % i j npages
+ /npages exch def
+ /j exch def
+ /i exch def
+ /str 10 string def
+ npages 1 gt {
+ gsave
+ coordfont setfont
+ 0 0 moveto
+ (\() show i str cvs show (,) show j str cvs show (\)) show
+ grestore
+ } if
+} bind def
+
+/set_font {
+ findfont exch
+ scalefont setfont
+} def
+
+% draw text fitted to its expected width
+/alignedtext { % width text
+ /text exch def
+ /width exch def
+ gsave
+ width 0 gt {
+ [] 0 setdash
+ text stringwidth pop width exch sub text length div 0 text ashow
+ } if
+ grestore
+} def
+
+/boxprim { % xcorner ycorner xsize ysize
+ 4 2 roll
+ moveto
+ 2 copy
+ exch 0 rlineto
+ 0 exch rlineto
+ pop neg 0 rlineto
+ closepath
+} bind def
+
+/ellipse_path {
+ /ry exch def
+ /rx exch def
+ /y exch def
+ /x exch def
+ matrix currentmatrix
+ newpath
+ x y translate
+ rx ry scale
+ 0 0 1 0 360 arc
+ setmatrix
+} bind def
+
+/endpage { showpage } bind def
+/showpage { } def
+
+/layercolorseq
+ [ % layer color sequence - darkest to lightest
+ [0 0 0]
+ [.2 .8 .8]
+ [.4 .8 .8]
+ [.6 .8 .8]
+ [.8 .8 .8]
+ ]
+def
+
+/layerlen layercolorseq length def
+
+/setlayer {/maxlayer exch def /curlayer exch def
+ layercolorseq curlayer 1 sub layerlen mod get
+ aload pop sethsbcolor
+ /nodecolor {nopcolor} def
+ /edgecolor {nopcolor} def
+ /graphcolor {nopcolor} def
+} bind def
+
+/onlayer { curlayer ne {invis} if } def
+
+/onlayers {
+ /myupper exch def
+ /mylower exch def
+ curlayer mylower lt
+ curlayer myupper gt
+ or
+ {invis} if
+} def
+
+/curlayer 0 def
+
+%%EndResource
+%%EndProlog
+%%BeginSetup
+14 default-font-family set_font
+1 setmiterlimit
+% /arrowlength 10 def
+% /arrowwidth 5 def
+
+% make sure pdfmark is harmless for PS-interpreters other than Distiller
+/pdfmark where {pop} {userdict /pdfmark /cleartomark load put} ifelse
+% make '<<' and '>>' safe on PS Level 1 devices
+/languagelevel where {pop languagelevel}{1} ifelse
+2 lt {
+ userdict (<<) cvn ([) cvn load put
+ userdict (>>) cvn ([) cvn load put
+} if
+
+%%EndSetup
+setupLatin1
+%%Page: 1 1
+%%PageBoundingBox: 36 36 576 248
+%%PageOrientation: Portrait
+0 0 1 beginpage
+gsave
+36 36 540 212 boxprim clip newpath
+1 1 set_scale 0 rotate 40 41 translate
+% ATC
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 0 moveto
+0 130 lineto
+56 130 lineto
+56 0 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+14 113.4 moveto 28 (ATC) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 104 moveto
+56 104 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+14 87.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 78 moveto
+56 78 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+8 61.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 52 moveto
+56 52 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+16.5 35.4 moveto 23 (2.0) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 26 moveto
+56 26 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+14 9.4 moveto 28 (ATC) alignedtext
+grestore
+% CGA
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 138.5 74 moveto
+138.5 204 lineto
+213.5 204 lineto
+213.5 74 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+160.5 187.4 moveto 31 (CGA) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 138.5 178 moveto
+213.5 178 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+162 161.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 138.5 152 moveto
+213.5 152 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+156 135.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 138.5 126 moveto
+213.5 126 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+164.5 109.4 moveto 23 (1.0) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 138.5 100 moveto
+213.5 100 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+146.5 83.4 moveto 59 (CTACGA) alignedtext
+grestore
+% ATC->CGA
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 56.03 93.22 moveto
+61.67 97.93 67.78 102.44 74 106 curveto
+90.6 115.52 110.32 122.71 127.98 127.92 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 127.52 131.42 moveto
+138.1 130.75 lineto
+129.41 124.68 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 127.52 131.42 moveto
+138.1 130.75 lineto
+129.41 124.68 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+74 130.4 moveto 46 (FR: [1]) alignedtext
+grestore
+% CTC
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 456.5 2 moveto
+456.5 132 lineto
+531.5 132 lineto
+531.5 2 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+480 115.4 moveto 28 (CTC) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 456.5 106 moveto
+531.5 106 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+480 89.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 456.5 80 moveto
+531.5 80 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+474 63.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 456.5 54 moveto
+531.5 54 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+482.5 37.4 moveto 23 (1.0) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 456.5 28 moveto
+531.5 28 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+464.5 11.4 moveto 59 (CTCAGA) alignedtext
+grestore
+% ATC->CTC
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 56.26 64.84 moveto
+115.28 64.54 255.97 64.02 374 65 curveto
+397.83 65.2 424.32 65.62 446.34 66.02 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 446.37 69.52 moveto
+456.44 66.21 lineto
+446.51 62.53 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 446.37 69.52 moveto
+456.44 66.21 lineto
+446.51 62.53 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+232 69.4 moveto 46 (FR: [2]) alignedtext
+grestore
+% CGA->ATC
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 138.23 96.51 moveto
+132.51 91.75 126.37 87.4 120 84 curveto
+103.67 75.29 83.75 70.57 66.62 68.01 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 66.74 64.5 moveto
+56.38 66.68 lineto
+65.84 71.44 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 66.74 64.5 moveto
+56.38 66.68 lineto
+65.84 71.44 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+74 89.4 moveto 46 (FR: [1]) alignedtext
+grestore
+% AGG
+gsave
+0 0 0.75294 nodecolor
+newpath 296 74 moveto
+296 204 lineto
+374 204 lineto
+374 74 lineto
+closepath fill
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 296 74 moveto
+296 204 lineto
+374 204 lineto
+374 74 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+318.5 187.4 moveto 33 (AGG) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 296 178 moveto
+374 178 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+321 161.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 296 152 moveto
+374 152 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+304 135.4 moveto 62 (~5':[2,1]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 296 126 moveto
+374 126 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+323.5 109.4 moveto 23 (2.0) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 296 100 moveto
+374 100 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+318.5 83.4 moveto 33 (AGG) alignedtext
+grestore
+% CGA->AGG
+gsave
+1 setlinewidth
+0.33333 1 1 edgecolor
+newpath 213.68 139 moveto
+235.28 139 262.64 139 285.9 139 curveto
+stroke
+0.33333 1 1 edgecolor
+newpath 285.93 142.5 moveto
+295.93 139 lineto
+285.93 135.5 lineto
+closepath fill
+1 setlinewidth
+solid
+0.33333 1 1 edgecolor
+newpath 285.93 142.5 moveto
+295.93 139 lineto
+285.93 135.5 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+232 144.4 moveto 46 (RF: [1]) alignedtext
+grestore
+% CTC->ATC
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 456.32 59.8 moveto
+405.49 50.92 312.06 37.5 232 42 curveto
+174.06 45.26 107.3 53.67 66.37 59.37 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 65.71 55.93 moveto
+56.3 60.79 lineto
+66.69 62.86 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 65.71 55.93 moveto
+56.3 60.79 lineto
+66.69 62.86 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+232 47.4 moveto 46 (FR: [2]) alignedtext
+grestore
+% CTC->AGG
+gsave
+1 setlinewidth
+0.33333 1 1 edgecolor
+newpath 456.33 73.13 moveto
+436.49 77.3 412.15 83.93 392 94 curveto
+388.86 95.57 385.73 97.33 382.64 99.22 curveto
+stroke
+0.33333 1 1 edgecolor
+newpath 380.52 96.43 moveto
+374.09 104.85 lineto
+384.36 102.28 lineto
+closepath fill
+1 setlinewidth
+solid
+0.33333 1 1 edgecolor
+newpath 380.52 96.43 moveto
+374.09 104.85 lineto
+384.36 102.28 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+392 99.4 moveto 46 (RF: [2]) alignedtext
+grestore
+% AGG->CGA
+gsave
+1 setlinewidth
+0.33333 1 1 edgecolor
+newpath 295.99 121.79 moveto
+290.07 119.81 283.94 118.11 278 117 curveto
+257.9 113.26 252.09 113.2 232 117 curveto
+229.16 117.54 226.28 118.22 223.41 119 curveto
+stroke
+0.33333 1 1 edgecolor
+newpath 222.21 115.7 moveto
+213.69 122 lineto
+224.28 122.39 lineto
+closepath fill
+1 setlinewidth
+solid
+0.33333 1 1 edgecolor
+newpath 222.21 115.7 moveto
+213.69 122 lineto
+224.28 122.39 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+232 122.4 moveto 46 (RF: [1]) alignedtext
+grestore
+% AGG->CTC
+gsave
+1 setlinewidth
+0.33333 1 1 edgecolor
+newpath 374.05 132.79 moveto
+393.92 128.65 418.02 122.06 438 112 curveto
+441.31 110.33 444.61 108.44 447.86 106.41 curveto
+stroke
+0.33333 1 1 edgecolor
+newpath 449.95 109.22 moveto
+456.29 100.73 lineto
+446.04 103.41 lineto
+closepath fill
+1 setlinewidth
+solid
+0.33333 1 1 edgecolor
+newpath 449.95 109.22 moveto
+456.29 100.73 lineto
+446.04 103.41 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+392 132.4 moveto 46 (RF: [2]) alignedtext
+grestore
+endpage
+showpage
+grestore
+%%PageTrailer
+%%EndPage: 1
+%%Trailer
+%%Pages: 1
+%%BoundingBox: 36 36 576 248
+end
+restore
+%%EOF
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/txt b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/txt
new file mode 100755
index 0000000..7d9905d
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/FRandRF/txt
@@ -0,0 +1,4 @@
+ATC {[] [{CGA:[1]}, {CTC:[2]}] [] [] {5':[], ~5':[]}ATC 2.0x}
+CTC {[] [{ATC:[2]}] [{AGG:[2]}] [] {5':[], ~5':[]}CTCAGA 1.0x}
+CGA {[] [{ATC:[1]}] [{AGG:[1]}] [] {5':[], ~5':[]}CTACGA 1.0x}
+AGG {[] [] [{CGA:[1]}, {CTC:[2]}] [] {5':[], ~5':[(2-0_0),(1-0_0)]}AGG 2.0x}
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/.txt.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/.txt.crc
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/.txt.crc
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/.part-0.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/.part-0.crc
new file mode 100644
index 0000000..40c2bbd
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/.part-0.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/.part-1.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/.part-1.crc
new file mode 100644
index 0000000..e529358
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/.part-1.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/.part-2.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/.part-2.crc
new file mode 100644
index 0000000..e864e87
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/.part-2.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/.part-3.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/.part-3.crc
new file mode 100644
index 0000000..323efa0
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/.part-3.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/.part-4.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/.part-4.crc
new file mode 100644
index 0000000..601146c
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/.part-4.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/.part-5.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/.part-5.crc
new file mode 100644
index 0000000..cb16a6b
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/.part-5.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/.part-6.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/.part-6.crc
new file mode 100644
index 0000000..bdcc755
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/.part-6.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/.part-7.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/.part-7.crc
new file mode 100644
index 0000000..5e69d86
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/.part-7.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/part-0 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/part-0
new file mode 100755
index 0000000..97686d5
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/part-0
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/part-1 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/part-1
new file mode 100755
index 0000000..f228f0b
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/part-1
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/part-2 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/part-2
new file mode 100755
index 0000000..95f4e7d
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/part-2
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/part-3 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/part-3
new file mode 100755
index 0000000..a573584
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/part-3
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/part-4 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/part-4
new file mode 100755
index 0000000..231f90d
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/part-4
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/part-5 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/part-5
new file mode 100755
index 0000000..99d0fa2
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/part-5
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/part-6 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/part-6
new file mode 100755
index 0000000..080a5d9
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/part-6
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/part-7 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/part-7
new file mode 100755
index 0000000..2910da3
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/bin/part-7
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/graphviz/result.ps b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/graphviz/result.ps
new file mode 100644
index 0000000..1d9fa6b
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/graphviz/result.ps
@@ -0,0 +1,594 @@
+%!PS-Adobe-3.0
+%%Creator: graphviz version 2.26.3 (20100126.1600)
+%%Title: G
+%%Pages: (atend)
+%%BoundingBox: (atend)
+%%EndComments
+save
+%%BeginProlog
+/DotDict 200 dict def
+DotDict begin
+
+/setupLatin1 {
+mark
+/EncodingVector 256 array def
+ EncodingVector 0
+
+ISOLatin1Encoding 0 255 getinterval putinterval
+EncodingVector 45 /hyphen put
+
+% Set up ISO Latin 1 character encoding
+/starnetISO {
+ dup dup findfont dup length dict begin
+ { 1 index /FID ne { def }{ pop pop } ifelse
+ } forall
+ /Encoding EncodingVector def
+ currentdict end definefont
+} def
+/Times-Roman starnetISO def
+/Times-Italic starnetISO def
+/Times-Bold starnetISO def
+/Times-BoldItalic starnetISO def
+/Helvetica starnetISO def
+/Helvetica-Oblique starnetISO def
+/Helvetica-Bold starnetISO def
+/Helvetica-BoldOblique starnetISO def
+/Courier starnetISO def
+/Courier-Oblique starnetISO def
+/Courier-Bold starnetISO def
+/Courier-BoldOblique starnetISO def
+cleartomark
+} bind def
+
+%%BeginResource: procset graphviz 0 0
+/coord-font-family /Times-Roman def
+/default-font-family /Times-Roman def
+/coordfont coord-font-family findfont 8 scalefont def
+
+/InvScaleFactor 1.0 def
+/set_scale {
+ dup 1 exch div /InvScaleFactor exch def
+ scale
+} bind def
+
+% styles
+/solid { [] 0 setdash } bind def
+/dashed { [9 InvScaleFactor mul dup ] 0 setdash } bind def
+/dotted { [1 InvScaleFactor mul 6 InvScaleFactor mul] 0 setdash } bind def
+/invis {/fill {newpath} def /stroke {newpath} def /show {pop newpath} def} bind def
+/bold { 2 setlinewidth } bind def
+/filled { } bind def
+/unfilled { } bind def
+/rounded { } bind def
+/diagonals { } bind def
+
+% hooks for setting color
+/nodecolor { sethsbcolor } bind def
+/edgecolor { sethsbcolor } bind def
+/graphcolor { sethsbcolor } bind def
+/nopcolor {pop pop pop} bind def
+
+/beginpage { % i j npages
+ /npages exch def
+ /j exch def
+ /i exch def
+ /str 10 string def
+ npages 1 gt {
+ gsave
+ coordfont setfont
+ 0 0 moveto
+ (\() show i str cvs show (,) show j str cvs show (\)) show
+ grestore
+ } if
+} bind def
+
+/set_font {
+ findfont exch
+ scalefont setfont
+} def
+
+% draw text fitted to its expected width
+/alignedtext { % width text
+ /text exch def
+ /width exch def
+ gsave
+ width 0 gt {
+ [] 0 setdash
+ text stringwidth pop width exch sub text length div 0 text ashow
+ } if
+ grestore
+} def
+
+/boxprim { % xcorner ycorner xsize ysize
+ 4 2 roll
+ moveto
+ 2 copy
+ exch 0 rlineto
+ 0 exch rlineto
+ pop neg 0 rlineto
+ closepath
+} bind def
+
+/ellipse_path {
+ /ry exch def
+ /rx exch def
+ /y exch def
+ /x exch def
+ matrix currentmatrix
+ newpath
+ x y translate
+ rx ry scale
+ 0 0 1 0 360 arc
+ setmatrix
+} bind def
+
+/endpage { showpage } bind def
+/showpage { } def
+
+/layercolorseq
+ [ % layer color sequence - darkest to lightest
+ [0 0 0]
+ [.2 .8 .8]
+ [.4 .8 .8]
+ [.6 .8 .8]
+ [.8 .8 .8]
+ ]
+def
+
+/layerlen layercolorseq length def
+
+/setlayer {/maxlayer exch def /curlayer exch def
+ layercolorseq curlayer 1 sub layerlen mod get
+ aload pop sethsbcolor
+ /nodecolor {nopcolor} def
+ /edgecolor {nopcolor} def
+ /graphcolor {nopcolor} def
+} bind def
+
+/onlayer { curlayer ne {invis} if } def
+
+/onlayers {
+ /myupper exch def
+ /mylower exch def
+ curlayer mylower lt
+ curlayer myupper gt
+ or
+ {invis} if
+} def
+
+/curlayer 0 def
+
+%%EndResource
+%%EndProlog
+%%BeginSetup
+14 default-font-family set_font
+1 setmiterlimit
+% /arrowlength 10 def
+% /arrowwidth 5 def
+
+% make sure pdfmark is harmless for PS-interpreters other than Distiller
+/pdfmark where {pop} {userdict /pdfmark /cleartomark load put} ifelse
+% make '<<' and '>>' safe on PS Level 1 devices
+/languagelevel where {pop languagelevel}{1} ifelse
+2 lt {
+ userdict (<<) cvn ([) cvn load put
+ userdict (>>) cvn ([) cvn load put
+} if
+
+%%EndSetup
+setupLatin1
+%%Page: 1 1
+%%PageBoundingBox: 36 36 514 248
+%%PageOrientation: Portrait
+0 0 1 beginpage
+gsave
+36 36 478 212 boxprim clip newpath
+1 1 set_scale 0 rotate 40 41 translate
+% TCA
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 0 moveto
+0 130 lineto
+56 130 lineto
+56 0 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+14 113.4 moveto 28 (TCA) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 104 moveto
+56 104 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+14 87.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 78 moveto
+56 78 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+8 61.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 52 moveto
+56 52 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+16.5 35.4 moveto 23 (1.0) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 26 moveto
+56 26 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+14 9.4 moveto 28 (TCA) alignedtext
+grestore
+% ATG
+gsave
+0 0 0.75294 nodecolor
+newpath 138 74 moveto
+138 204 lineto
+194 204 lineto
+194 74 lineto
+closepath fill
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 138 74 moveto
+138 204 lineto
+194 204 lineto
+194 74 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+151 187.4 moveto 30 (ATG) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 138 178 moveto
+194 178 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+147.5 161.4 moveto 37 (5':[2]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 138 152 moveto
+194 152 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+146 135.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 138 126 moveto
+194 126 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+154.5 109.4 moveto 23 (2.0) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 138 100 moveto
+194 100 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+151 83.4 moveto 30 (ATG) alignedtext
+grestore
+% TCA->ATG
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 56.12 93.06 moveto
+61.75 97.78 67.84 102.34 74 106 curveto
+90.71 115.93 110.88 123.58 128.07 129 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 127.21 132.4 moveto
+137.8 131.94 lineto
+129.24 125.7 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 127.21 132.4 moveto
+137.8 131.94 lineto
+129.24 125.7 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+74 130.4 moveto 46 (FR: [2]) alignedtext
+grestore
+% ATT
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 414 2 moveto
+414 132 lineto
+470 132 lineto
+470 2 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+428 115.4 moveto 28 (ATT) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 414 106 moveto
+470 106 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+428 89.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 414 80 moveto
+470 80 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+422 63.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 414 54 moveto
+470 54 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+430.5 37.4 moveto 23 (0.0) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 414 28 moveto
+470 28 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+427 11.4 moveto 30 (ATG) alignedtext
+grestore
+% TCA->ATT
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 56.22 64.29 moveto
+62.09 64.17 68.25 64.06 74 64 curveto
+94.44 63.78 99.56 63.95 120 64 curveto
+214.22 64.22 237.78 63.92 332 65 curveto
+355.85 65.27 382.62 65.76 403.77 66.18 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 403.9 69.68 moveto
+413.97 66.39 lineto
+404.04 62.68 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 403.9 69.68 moveto
+413.97 66.39 lineto
+404.04 62.68 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+212 69.4 moveto 46 (FR: [0]) alignedtext
+grestore
+% ATG->TCA
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 137.93 98.66 moveto
+132.54 93.06 126.52 87.9 120 84 curveto
+104 74.43 83.96 69.62 66.66 67.23 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 66.64 63.7 moveto
+56.31 66.03 lineto
+65.84 70.65 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 66.64 63.7 moveto
+56.31 66.03 lineto
+65.84 70.65 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+74 89.4 moveto 46 (FR: [2]) alignedtext
+grestore
+% ACA
+gsave
+0 0 0.75294 nodecolor
+newpath 276 74 moveto
+276 204 lineto
+332 204 lineto
+332 74 lineto
+closepath fill
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 276 74 moveto
+276 204 lineto
+332 204 lineto
+332 74 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+289 187.4 moveto 30 (ACA) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 276 178 moveto
+332 178 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+285.5 161.4 moveto 37 (5':[1]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 276 152 moveto
+332 152 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+284 135.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 276 126 moveto
+332 126 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+292.5 109.4 moveto 23 (1.0) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 276 100 moveto
+332 100 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+289 83.4 moveto 30 (ACA) alignedtext
+grestore
+% ATG->ACA
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 194.26 139 moveto
+214.82 139 242.89 139 265.5 139 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 265.78 142.5 moveto
+275.78 139 lineto
+265.78 135.5 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 265.78 142.5 moveto
+275.78 139 lineto
+265.78 135.5 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+212 144.4 moveto 46 (FR: [1]) alignedtext
+grestore
+% ATT->TCA
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 413.75 61.95 moveto
+377.74 55.8 313.48 45.75 258 42 curveto
+176.06 36.46 155.47 48.67 74 59 curveto
+71.48 59.32 68.89 59.65 66.28 59.99 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 65.68 56.53 moveto
+56.22 61.29 lineto
+66.58 63.48 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 65.68 56.53 moveto
+56.22 61.29 lineto
+66.58 63.48 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+212 47.4 moveto 46 (FR: [2]) alignedtext
+grestore
+% ATT->ACA
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 413.81 68.98 moveto
+394.71 71.35 369.5 76.56 350 88 curveto
+346.51 90.05 343.14 92.44 339.92 95.07 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 337.33 92.69 moveto
+332.23 101.97 lineto
+342.01 97.9 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 337.33 92.69 moveto
+332.23 101.97 lineto
+342.01 97.9 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+350 93.4 moveto 46 (FR: [1]) alignedtext
+grestore
+% ACA->ATG
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 275.89 124.63 moveto
+270.11 122.3 263.97 120.24 258 119 curveto
+237.98 114.84 232.02 114.84 212 119 curveto
+209.2 119.58 206.37 120.34 203.55 121.23 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 202.33 117.95 moveto
+194.11 124.63 lineto
+204.71 124.53 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 202.33 117.95 moveto
+194.11 124.63 lineto
+204.71 124.53 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+212 124.4 moveto 46 (FR: [1]) alignedtext
+grestore
+% ACA->ATT
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 332.31 133.53 moveto
+351.23 129.06 376.19 121.57 396 110 curveto
+399.41 108.01 402.77 105.73 406.03 103.27 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 408.34 105.91 moveto
+413.89 96.89 lineto
+403.92 100.47 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 408.34 105.91 moveto
+413.89 96.89 lineto
+403.92 100.47 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+350 133.4 moveto 46 (FR: [0]) alignedtext
+grestore
+endpage
+showpage
+grestore
+%%PageTrailer
+%%EndPage: 1
+%%Trailer
+%%Pages: 1
+%%BoundingBox: 36 36 514 248
+end
+restore
+%%EOF
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/txt b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/txt
new file mode 100755
index 0000000..de2b9ec
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/InvalidBubble/txt
@@ -0,0 +1,4 @@
+TCA {[] [{ATG:[2]}, {ATT:[0]}] [] [] {5':[], ~5':[]}TCA 1.0x}
+ACA {[] [{ATG:[1]}, {ATT:[0]}] [] [] {5':[(1-0_0)], ~5':[]}ACA 1.0x}
+ATG {[] [{TCA:[2]}, {ACA:[1]}] [] [] {5':[(2-0_0)], ~5':[]}ATG 2.0x}
+ATT {[] [{TCA:[2]}, {ACA:[1]}] [] [] {5':[], ~5':[]}ATG 0.0x}
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/.txt.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/.txt.crc
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/.txt.crc
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/.part-0.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/.part-0.crc
new file mode 100644
index 0000000..fb385c6
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/.part-0.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/.part-1.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/.part-1.crc
new file mode 100644
index 0000000..dbc0e18
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/.part-1.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/.part-2.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/.part-2.crc
new file mode 100644
index 0000000..fc18000
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/.part-2.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/.part-3.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/.part-3.crc
new file mode 100644
index 0000000..b8a2fd7
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/.part-3.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/.part-4.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/.part-4.crc
new file mode 100644
index 0000000..d9cd959
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/.part-4.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/.part-5.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/.part-5.crc
new file mode 100644
index 0000000..4895b2a
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/.part-5.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/.part-6.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/.part-6.crc
new file mode 100644
index 0000000..2331529
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/.part-6.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/.part-7.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/.part-7.crc
new file mode 100644
index 0000000..3413255
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/.part-7.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/part-0 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/part-0
new file mode 100755
index 0000000..8053fa0
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/part-0
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/part-1 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/part-1
new file mode 100755
index 0000000..79ca01a
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/part-1
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/part-2 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/part-2
new file mode 100755
index 0000000..5bd37ce
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/part-2
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/part-3 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/part-3
new file mode 100755
index 0000000..7a24753
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/part-3
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/part-4 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/part-4
new file mode 100755
index 0000000..d46ac97
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/part-4
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/part-5 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/part-5
new file mode 100755
index 0000000..0ff23a5
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/part-5
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/part-6 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/part-6
new file mode 100755
index 0000000..add2670
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/part-6
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/part-7 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/part-7
new file mode 100755
index 0000000..09c86a2
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/bin/part-7
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/graphviz/result.ps b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/graphviz/result.ps
new file mode 100644
index 0000000..f3d9a12
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/graphviz/result.ps
@@ -0,0 +1,581 @@
+%!PS-Adobe-3.0
+%%Creator: graphviz version 2.26.3 (20100126.1600)
+%%Title: G
+%%Pages: (atend)
+%%BoundingBox: (atend)
+%%EndComments
+save
+%%BeginProlog
+/DotDict 200 dict def
+DotDict begin
+
+/setupLatin1 {
+mark
+/EncodingVector 256 array def
+ EncodingVector 0
+
+ISOLatin1Encoding 0 255 getinterval putinterval
+EncodingVector 45 /hyphen put
+
+% Set up ISO Latin 1 character encoding
+/starnetISO {
+ dup dup findfont dup length dict begin
+ { 1 index /FID ne { def }{ pop pop } ifelse
+ } forall
+ /Encoding EncodingVector def
+ currentdict end definefont
+} def
+/Times-Roman starnetISO def
+/Times-Italic starnetISO def
+/Times-Bold starnetISO def
+/Times-BoldItalic starnetISO def
+/Helvetica starnetISO def
+/Helvetica-Oblique starnetISO def
+/Helvetica-Bold starnetISO def
+/Helvetica-BoldOblique starnetISO def
+/Courier starnetISO def
+/Courier-Oblique starnetISO def
+/Courier-Bold starnetISO def
+/Courier-BoldOblique starnetISO def
+cleartomark
+} bind def
+
+%%BeginResource: procset graphviz 0 0
+/coord-font-family /Times-Roman def
+/default-font-family /Times-Roman def
+/coordfont coord-font-family findfont 8 scalefont def
+
+/InvScaleFactor 1.0 def
+/set_scale {
+ dup 1 exch div /InvScaleFactor exch def
+ scale
+} bind def
+
+% styles
+/solid { [] 0 setdash } bind def
+/dashed { [9 InvScaleFactor mul dup ] 0 setdash } bind def
+/dotted { [1 InvScaleFactor mul 6 InvScaleFactor mul] 0 setdash } bind def
+/invis {/fill {newpath} def /stroke {newpath} def /show {pop newpath} def} bind def
+/bold { 2 setlinewidth } bind def
+/filled { } bind def
+/unfilled { } bind def
+/rounded { } bind def
+/diagonals { } bind def
+
+% hooks for setting color
+/nodecolor { sethsbcolor } bind def
+/edgecolor { sethsbcolor } bind def
+/graphcolor { sethsbcolor } bind def
+/nopcolor {pop pop pop} bind def
+
+/beginpage { % i j npages
+ /npages exch def
+ /j exch def
+ /i exch def
+ /str 10 string def
+ npages 1 gt {
+ gsave
+ coordfont setfont
+ 0 0 moveto
+ (\() show i str cvs show (,) show j str cvs show (\)) show
+ grestore
+ } if
+} bind def
+
+/set_font {
+ findfont exch
+ scalefont setfont
+} def
+
+% draw text fitted to its expected width
+/alignedtext { % width text
+ /text exch def
+ /width exch def
+ gsave
+ width 0 gt {
+ [] 0 setdash
+ text stringwidth pop width exch sub text length div 0 text ashow
+ } if
+ grestore
+} def
+
+/boxprim { % xcorner ycorner xsize ysize
+ 4 2 roll
+ moveto
+ 2 copy
+ exch 0 rlineto
+ 0 exch rlineto
+ pop neg 0 rlineto
+ closepath
+} bind def
+
+/ellipse_path {
+ /ry exch def
+ /rx exch def
+ /y exch def
+ /x exch def
+ matrix currentmatrix
+ newpath
+ x y translate
+ rx ry scale
+ 0 0 1 0 360 arc
+ setmatrix
+} bind def
+
+/endpage { showpage } bind def
+/showpage { } def
+
+/layercolorseq
+ [ % layer color sequence - darkest to lightest
+ [0 0 0]
+ [.2 .8 .8]
+ [.4 .8 .8]
+ [.6 .8 .8]
+ [.8 .8 .8]
+ ]
+def
+
+/layerlen layercolorseq length def
+
+/setlayer {/maxlayer exch def /curlayer exch def
+ layercolorseq curlayer 1 sub layerlen mod get
+ aload pop sethsbcolor
+ /nodecolor {nopcolor} def
+ /edgecolor {nopcolor} def
+ /graphcolor {nopcolor} def
+} bind def
+
+/onlayer { curlayer ne {invis} if } def
+
+/onlayers {
+ /myupper exch def
+ /mylower exch def
+ curlayer mylower lt
+ curlayer myupper gt
+ or
+ {invis} if
+} def
+
+/curlayer 0 def
+
+%%EndResource
+%%EndProlog
+%%BeginSetup
+14 default-font-family set_font
+1 setmiterlimit
+% /arrowlength 10 def
+% /arrowwidth 5 def
+
+% make sure pdfmark is harmless for PS-interpreters other than Distiller
+/pdfmark where {pop} {userdict /pdfmark /cleartomark load put} ifelse
+% make '<<' and '>>' safe on PS Level 1 devices
+/languagelevel where {pop languagelevel}{1} ifelse
+2 lt {
+ userdict (<<) cvn ([) cvn load put
+ userdict (>>) cvn ([) cvn load put
+} if
+
+%%EndSetup
+setupLatin1
+%%Page: 1 1
+%%PageBoundingBox: 36 36 596 248
+%%PageOrientation: Portrait
+0 0 1 beginpage
+gsave
+36 36 560 212 boxprim clip newpath
+1 1 set_scale 0 rotate 40 41 translate
+% GGA
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 0 moveto
+0 130 lineto
+56 130 lineto
+56 0 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+11.5 113.4 moveto 33 (GGA) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 104 moveto
+56 104 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+14 87.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 78 moveto
+56 78 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+8 61.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 52 moveto
+56 52 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+16.5 35.4 moveto 23 (2.0) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 26 moveto
+56 26 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+11.5 9.4 moveto 33 (GGA) alignedtext
+grestore
+% CCG
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 138 74 moveto
+138 204 lineto
+226 204 lineto
+226 74 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+166.5 187.4 moveto 31 (CCG) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 138 178 moveto
+226 178 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+168 161.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 138 152 moveto
+226 152 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+162 135.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 138 126 moveto
+226 126 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+170.5 109.4 moveto 23 (1.0) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 138 100 moveto
+226 100 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+146 83.4 moveto 72 (CCAGCCG) alignedtext
+grestore
+% GGA->CCG
+gsave
+1 setlinewidth
+0.33333 1 1 edgecolor
+newpath 56.23 93.51 moveto
+61.81 98.14 67.85 102.54 74 106 curveto
+90.65 115.37 110.28 122.38 128.2 127.48 curveto
+stroke
+0.33333 1 1 edgecolor
+newpath 127.38 130.89 moveto
+137.95 130.12 lineto
+129.21 124.13 lineto
+closepath fill
+1 setlinewidth
+solid
+0.33333 1 1 edgecolor
+newpath 127.38 130.89 moveto
+137.95 130.12 lineto
+129.21 124.13 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+74 129.4 moveto 46 (RF: [2]) alignedtext
+grestore
+% AGG
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 460.5 2 moveto
+460.5 132 lineto
+551.5 132 lineto
+551.5 2 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+489.5 115.4 moveto 33 (AGG) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 460.5 106 moveto
+551.5 106 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+492 89.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 460.5 80 moveto
+551.5 80 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+486 63.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 460.5 54 moveto
+551.5 54 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+494.5 37.4 moveto 23 (1.0) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 460.5 28 moveto
+551.5 28 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+468.5 11.4 moveto 75 (CGAAAGG) alignedtext
+grestore
+% GGA->AGG
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 56.42 64.85 moveto
+115.78 64.58 257.28 64.09 376 65 curveto
+400.27 65.19 427.09 65.57 450.03 65.95 curveto
+stroke
+0 1 1 edgecolor
+newpath 450.22 69.45 moveto
+460.28 66.12 lineto
+450.34 62.46 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 450.22 69.45 moveto
+460.28 66.12 lineto
+450.34 62.46 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+244 69.4 moveto 48 (RR: [1]) alignedtext
+grestore
+% CCG->GGA
+gsave
+1 setlinewidth
+0.33333 1 1 edgecolor
+newpath 137.95 95.21 moveto
+132.21 90.96 126.17 87.09 120 84 curveto
+103.46 75.71 83.51 71.03 66.42 68.4 curveto
+stroke
+0.33333 1 1 edgecolor
+newpath 66.59 64.89 moveto
+56.21 67.01 lineto
+65.64 71.83 lineto
+closepath fill
+1 setlinewidth
+solid
+0.33333 1 1 edgecolor
+newpath 66.59 64.89 moveto
+56.21 67.01 lineto
+65.64 71.83 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+74 89.4 moveto 46 (RF: [2]) alignedtext
+grestore
+% ACG
+gsave
+0 0 0.75294 nodecolor
+newpath 310 74 moveto
+310 204 lineto
+376 204 lineto
+376 74 lineto
+closepath fill
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 310 74 moveto
+310 204 lineto
+376 204 lineto
+376 74 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+327.5 187.4 moveto 31 (ACG) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 310 178 moveto
+376 178 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+318 161.4 moveto 50 (5':[2,1]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 310 152 moveto
+376 152 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+323 135.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 310 126 moveto
+376 126 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+331.5 109.4 moveto 23 (2.0) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 310 100 moveto
+376 100 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+327.5 83.4 moveto 31 (ACG) alignedtext
+grestore
+% CCG->ACG
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 226.42 139 moveto
+249.34 139 277.19 139 299.91 139 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 299.96 142.5 moveto
+309.96 139 lineto
+299.96 135.5 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 299.96 142.5 moveto
+309.96 139 lineto
+299.96 135.5 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+245 144.4 moveto 46 (FR: [2]) alignedtext
+grestore
+% AGG->GGA
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 460.22 60.09 moveto
+416.98 53.93 350.25 45.39 292 42 curveto
+194.95 36.35 170.66 49.63 74 60 curveto
+71.48 60.27 68.89 60.55 66.28 60.83 curveto
+stroke
+0 0 0 edgecolor
+newpath 65.78 57.36 moveto
+56.22 61.92 lineto
+66.54 64.32 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 65.78 57.36 moveto
+56.22 61.92 lineto
+66.54 64.32 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+245.5 47.4 moveto 45 (FF: [1]) alignedtext
+grestore
+% AGG->ACG
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 460.36 69.37 moveto
+439.2 71.98 414.3 77.29 394 88 curveto
+390.65 89.77 387.37 91.83 384.21 94.1 curveto
+stroke
+0 1 1 edgecolor
+newpath 381.78 91.55 moveto
+376.1 100.5 lineto
+386.12 97.05 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 381.78 91.55 moveto
+376.1 100.5 lineto
+386.12 97.05 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+394 93.4 moveto 48 (RR: [1]) alignedtext
+grestore
+% ACG->CCG
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 309.78 123.94 moveto
+303.97 121.89 297.89 120.11 292 119 curveto
+271.04 115.04 265.07 115.69 244 119 curveto
+241.37 119.41 238.69 119.92 236.01 120.5 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 235.18 117.1 moveto
+226.3 122.88 lineto
+236.84 123.9 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 235.18 117.1 moveto
+226.3 122.88 lineto
+236.84 123.9 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+245 124.4 moveto 46 (FR: [2]) alignedtext
+grestore
+% ACG->AGG
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 376.02 132.02 moveto
+395.72 127.2 420.92 119.88 442 110 curveto
+445.12 108.54 448.27 106.93 451.4 105.23 curveto
+stroke
+0 0 0 edgecolor
+newpath 453.22 108.22 moveto
+460.14 100.2 lineto
+449.73 102.15 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 453.22 108.22 moveto
+460.14 100.2 lineto
+449.73 102.15 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+395.5 132.4 moveto 45 (FF: [1]) alignedtext
+grestore
+endpage
+showpage
+grestore
+%%PageTrailer
+%%EndPage: 1
+%%Trailer
+%%Pages: 1
+%%BoundingBox: 36 36 596 248
+end
+restore
+%%EOF
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/txt b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/txt
new file mode 100755
index 0000000..7c8128f
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoL/txt
@@ -0,0 +1,4 @@
+GGA {[] [] [{CCG:[2]}] [{AGG:[1]}] {5':[], ~5':[]}GGA 2.0x}
+ACG {[{AGG:[1]}] [{CCG:[2]}] [] [] {5':[(2-0_0),(1-0_0)], ~5':[]}ACG 2.0x}
+CCG {[] [{ACG:[2]}] [{GGA:[2]}] [] {5':[], ~5':[]}CCAGCCG 1.0x}
+AGG {[{GGA:[1]}] [] [] [{ACG:[1]}] {5':[], ~5':[]}CGAAAGG 1.0x}
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/.txt.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/.txt.crc
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/.txt.crc
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/.part-0.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/.part-0.crc
new file mode 100644
index 0000000..cce9b15
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/.part-0.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/.part-1.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/.part-1.crc
new file mode 100644
index 0000000..31969cb
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/.part-1.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/.part-2.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/.part-2.crc
new file mode 100644
index 0000000..11598fe
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/.part-2.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/.part-3.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/.part-3.crc
new file mode 100644
index 0000000..ff3e7c0
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/.part-3.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/.part-4.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/.part-4.crc
new file mode 100644
index 0000000..de1d28f
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/.part-4.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/.part-5.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/.part-5.crc
new file mode 100644
index 0000000..7c7cb30
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/.part-5.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/.part-6.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/.part-6.crc
new file mode 100644
index 0000000..e5aa322
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/.part-6.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/.part-7.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/.part-7.crc
new file mode 100644
index 0000000..3ec76e0
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/.part-7.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/part-0 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/part-0
new file mode 100755
index 0000000..678221d
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/part-0
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/part-1 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/part-1
new file mode 100755
index 0000000..bef0b92
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/part-1
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/part-2 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/part-2
new file mode 100755
index 0000000..82226e6
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/part-2
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/part-3 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/part-3
new file mode 100755
index 0000000..2c6dde0
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/part-3
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/part-4 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/part-4
new file mode 100755
index 0000000..804a903
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/part-4
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/part-5 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/part-5
new file mode 100755
index 0000000..97cc676
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/part-5
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/part-6 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/part-6
new file mode 100755
index 0000000..654c556
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/part-6
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/part-7 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/part-7
new file mode 100755
index 0000000..b3d7878
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/bin/part-7
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/graphviz/result.ps b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/graphviz/result.ps
new file mode 100644
index 0000000..6e6fe14
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/graphviz/result.ps
@@ -0,0 +1,581 @@
+%!PS-Adobe-3.0
+%%Creator: graphviz version 2.26.3 (20100126.1600)
+%%Title: G
+%%Pages: (atend)
+%%BoundingBox: (atend)
+%%EndComments
+save
+%%BeginProlog
+/DotDict 200 dict def
+DotDict begin
+
+/setupLatin1 {
+mark
+/EncodingVector 256 array def
+ EncodingVector 0
+
+ISOLatin1Encoding 0 255 getinterval putinterval
+EncodingVector 45 /hyphen put
+
+% Set up ISO Latin 1 character encoding
+/starnetISO {
+ dup dup findfont dup length dict begin
+ { 1 index /FID ne { def }{ pop pop } ifelse
+ } forall
+ /Encoding EncodingVector def
+ currentdict end definefont
+} def
+/Times-Roman starnetISO def
+/Times-Italic starnetISO def
+/Times-Bold starnetISO def
+/Times-BoldItalic starnetISO def
+/Helvetica starnetISO def
+/Helvetica-Oblique starnetISO def
+/Helvetica-Bold starnetISO def
+/Helvetica-BoldOblique starnetISO def
+/Courier starnetISO def
+/Courier-Oblique starnetISO def
+/Courier-Bold starnetISO def
+/Courier-BoldOblique starnetISO def
+cleartomark
+} bind def
+
+%%BeginResource: procset graphviz 0 0
+/coord-font-family /Times-Roman def
+/default-font-family /Times-Roman def
+/coordfont coord-font-family findfont 8 scalefont def
+
+/InvScaleFactor 1.0 def
+/set_scale {
+ dup 1 exch div /InvScaleFactor exch def
+ scale
+} bind def
+
+% styles
+/solid { [] 0 setdash } bind def
+/dashed { [9 InvScaleFactor mul dup ] 0 setdash } bind def
+/dotted { [1 InvScaleFactor mul 6 InvScaleFactor mul] 0 setdash } bind def
+/invis {/fill {newpath} def /stroke {newpath} def /show {pop newpath} def} bind def
+/bold { 2 setlinewidth } bind def
+/filled { } bind def
+/unfilled { } bind def
+/rounded { } bind def
+/diagonals { } bind def
+
+% hooks for setting color
+/nodecolor { sethsbcolor } bind def
+/edgecolor { sethsbcolor } bind def
+/graphcolor { sethsbcolor } bind def
+/nopcolor {pop pop pop} bind def
+
+/beginpage { % i j npages
+ /npages exch def
+ /j exch def
+ /i exch def
+ /str 10 string def
+ npages 1 gt {
+ gsave
+ coordfont setfont
+ 0 0 moveto
+ (\() show i str cvs show (,) show j str cvs show (\)) show
+ grestore
+ } if
+} bind def
+
+/set_font {
+ findfont exch
+ scalefont setfont
+} def
+
+% draw text fitted to its expected width
+/alignedtext { % width text
+ /text exch def
+ /width exch def
+ gsave
+ width 0 gt {
+ [] 0 setdash
+ text stringwidth pop width exch sub text length div 0 text ashow
+ } if
+ grestore
+} def
+
+/boxprim { % xcorner ycorner xsize ysize
+ 4 2 roll
+ moveto
+ 2 copy
+ exch 0 rlineto
+ 0 exch rlineto
+ pop neg 0 rlineto
+ closepath
+} bind def
+
+/ellipse_path {
+ /ry exch def
+ /rx exch def
+ /y exch def
+ /x exch def
+ matrix currentmatrix
+ newpath
+ x y translate
+ rx ry scale
+ 0 0 1 0 360 arc
+ setmatrix
+} bind def
+
+/endpage { showpage } bind def
+/showpage { } def
+
+/layercolorseq
+ [ % layer color sequence - darkest to lightest
+ [0 0 0]
+ [.2 .8 .8]
+ [.4 .8 .8]
+ [.6 .8 .8]
+ [.8 .8 .8]
+ ]
+def
+
+/layerlen layercolorseq length def
+
+/setlayer {/maxlayer exch def /curlayer exch def
+ layercolorseq curlayer 1 sub layerlen mod get
+ aload pop sethsbcolor
+ /nodecolor {nopcolor} def
+ /edgecolor {nopcolor} def
+ /graphcolor {nopcolor} def
+} bind def
+
+/onlayer { curlayer ne {invis} if } def
+
+/onlayers {
+ /myupper exch def
+ /mylower exch def
+ curlayer mylower lt
+ curlayer myupper gt
+ or
+ {invis} if
+} def
+
+/curlayer 0 def
+
+%%EndResource
+%%EndProlog
+%%BeginSetup
+14 default-font-family set_font
+1 setmiterlimit
+% /arrowlength 10 def
+% /arrowwidth 5 def
+
+% make sure pdfmark is harmless for PS-interpreters other than Distiller
+/pdfmark where {pop} {userdict /pdfmark /cleartomark load put} ifelse
+% make '<<' and '>>' safe on PS Level 1 devices
+/languagelevel where {pop languagelevel}{1} ifelse
+2 lt {
+ userdict (<<) cvn ([) cvn load put
+ userdict (>>) cvn ([) cvn load put
+} if
+
+%%EndSetup
+setupLatin1
+%%Page: 1 1
+%%PageBoundingBox: 36 36 596 248
+%%PageOrientation: Portrait
+0 0 1 beginpage
+gsave
+36 36 560 212 boxprim clip newpath
+1 1 set_scale 0 rotate 40 41 translate
+% ACC
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 0 moveto
+0 130 lineto
+56 130 lineto
+56 0 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+13 113.4 moveto 30 (ACC) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 104 moveto
+56 104 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+14 87.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 78 moveto
+56 78 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+8 61.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 52 moveto
+56 52 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+16.5 35.4 moveto 23 (2.0) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 26 moveto
+56 26 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+13 9.4 moveto 30 (ACC) alignedtext
+grestore
+% CCG
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 140 74 moveto
+140 204 lineto
+228 204 lineto
+228 74 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+168.5 187.4 moveto 31 (CCG) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 140 178 moveto
+228 178 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+170 161.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 140 152 moveto
+228 152 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+164 135.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 140 126 moveto
+228 126 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+172.5 109.4 moveto 23 (1.0) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 140 100 moveto
+228 100 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+148 83.4 moveto 72 (CCAGCCG) alignedtext
+grestore
+% ACC->CCG
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 56.22 93.54 moveto
+61.79 98.16 67.84 102.55 74 106 curveto
+91.26 115.65 111.66 122.77 130.17 127.88 curveto
+stroke
+0 0 0 edgecolor
+newpath 129.38 131.29 moveto
+139.94 130.45 lineto
+131.15 124.52 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 129.38 131.29 moveto
+139.94 130.45 lineto
+131.15 124.52 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+75.5 130.4 moveto 45 (FF: [2]) alignedtext
+grestore
+% AGG
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 460.5 2 moveto
+460.5 132 lineto
+551.5 132 lineto
+551.5 2 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+489.5 115.4 moveto 33 (AGG) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 460.5 106 moveto
+551.5 106 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+492 89.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 460.5 80 moveto
+551.5 80 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+486 63.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 460.5 54 moveto
+551.5 54 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+494.5 37.4 moveto 23 (1.0) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 460.5 28 moveto
+551.5 28 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+468.5 11.4 moveto 75 (CGAAAGG) alignedtext
+grestore
+% ACC->AGG
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 56.42 64.85 moveto
+115.78 64.58 257.28 64.09 376 65 curveto
+400.27 65.19 427.09 65.57 450.03 65.95 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 450.22 69.45 moveto
+460.28 66.12 lineto
+450.34 62.46 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 450.22 69.45 moveto
+460.28 66.12 lineto
+450.34 62.46 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+246 69.4 moveto 46 (FR: [1]) alignedtext
+grestore
+% CCG->ACC
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 139.96 95.18 moveto
+134.22 90.94 128.18 87.08 122 84 curveto
+104.81 75.43 84.03 70.72 66.38 68.14 curveto
+stroke
+0 1 1 edgecolor
+newpath 66.76 64.66 moveto
+56.4 66.85 lineto
+65.87 71.61 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 66.76 64.66 moveto
+56.4 66.85 lineto
+65.87 71.61 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+74 89.4 moveto 48 (RR: [2]) alignedtext
+grestore
+% ACG
+gsave
+0 0 0.75294 nodecolor
+newpath 310 74 moveto
+310 204 lineto
+376 204 lineto
+376 74 lineto
+closepath fill
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 310 74 moveto
+310 204 lineto
+376 204 lineto
+376 74 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+327.5 187.4 moveto 31 (ACG) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 310 178 moveto
+376 178 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+318 161.4 moveto 50 (5':[2,1]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 310 152 moveto
+376 152 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+323 135.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 310 126 moveto
+376 126 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+331.5 109.4 moveto 23 (2.0) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 310 100 moveto
+376 100 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+327.5 83.4 moveto 31 (ACG) alignedtext
+grestore
+% CCG->ACG
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 228.29 139 moveto
+250.58 139 277.5 139 299.66 139 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 299.79 142.5 moveto
+309.79 139 lineto
+299.79 135.5 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 299.79 142.5 moveto
+309.79 139 lineto
+299.79 135.5 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+246 144.4 moveto 46 (FR: [2]) alignedtext
+grestore
+% AGG->ACC
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 460.22 60.09 moveto
+416.98 53.93 350.25 45.39 292 42 curveto
+194.95 36.35 170.67 49.69 74 60 curveto
+71.48 60.27 68.89 60.55 66.28 60.83 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 65.78 57.36 moveto
+56.22 61.91 lineto
+66.54 64.32 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 65.78 57.36 moveto
+56.22 61.91 lineto
+66.54 64.32 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+246 47.4 moveto 46 (FR: [1]) alignedtext
+grestore
+% AGG->ACG
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 460.36 69.37 moveto
+439.2 71.98 414.3 77.29 394 88 curveto
+390.65 89.77 387.37 91.83 384.21 94.1 curveto
+stroke
+0 1 1 edgecolor
+newpath 381.78 91.55 moveto
+376.1 100.5 lineto
+386.12 97.05 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 381.78 91.55 moveto
+376.1 100.5 lineto
+386.12 97.05 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+394 93.4 moveto 48 (RR: [1]) alignedtext
+grestore
+% ACG->CCG
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 309.78 123.94 moveto
+303.97 121.89 297.89 120.11 292 119 curveto
+271.91 115.2 266.2 115.82 246 119 curveto
+243.37 119.41 240.69 119.92 238.01 120.5 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 237.18 117.1 moveto
+228.3 122.88 lineto
+238.84 123.9 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 237.18 117.1 moveto
+228.3 122.88 lineto
+238.84 123.9 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+246 124.4 moveto 46 (FR: [2]) alignedtext
+grestore
+% ACG->AGG
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 376.02 132.02 moveto
+395.72 127.2 420.92 119.88 442 110 curveto
+445.12 108.54 448.27 106.93 451.4 105.23 curveto
+stroke
+0 0 0 edgecolor
+newpath 453.22 108.22 moveto
+460.14 100.2 lineto
+449.73 102.15 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 453.22 108.22 moveto
+460.14 100.2 lineto
+449.73 102.15 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+395.5 132.4 moveto 45 (FF: [1]) alignedtext
+grestore
+endpage
+showpage
+grestore
+%%PageTrailer
+%%EndPage: 1
+%%Trailer
+%%Pages: 1
+%%BoundingBox: 36 36 596 248
+end
+restore
+%%EOF
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/txt b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/txt
new file mode 100755
index 0000000..d3a6adb
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/LtoR/txt
@@ -0,0 +1,4 @@
+ACC {[{CCG:[2]}] [{AGG:[1]}] [] [] {5':[], ~5':[]}ACC 2.0x}
+ACG {[{AGG:[1]}] [{CCG:[2]}] [] [] {5':[(2-0_0),(1-0_0)], ~5':[]}ACG 2.0x}
+CCG {[] [{ACG:[2]}] [] [{ACC:[2]}] {5':[], ~5':[]}CCAGCCG 1.0x}
+AGG {[] [{ACC:[1]}] [] [{ACG:[1]}] {5':[], ~5':[]}CGAAAGG 1.0x}
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/.txt.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/.txt.crc
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/.txt.crc
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/.part-0.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/.part-0.crc
new file mode 100644
index 0000000..349f617
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/.part-0.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/.part-1.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/.part-1.crc
new file mode 100644
index 0000000..4a6c688
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/.part-1.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/.part-2.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/.part-2.crc
new file mode 100644
index 0000000..e0618e6
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/.part-2.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/.part-3.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/.part-3.crc
new file mode 100644
index 0000000..b9bfd04
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/.part-3.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/.part-4.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/.part-4.crc
new file mode 100644
index 0000000..9a31a14
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/.part-4.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/.part-5.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/.part-5.crc
new file mode 100644
index 0000000..80cde45
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/.part-5.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/.part-6.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/.part-6.crc
new file mode 100644
index 0000000..be699c7
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/.part-6.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/.part-7.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/.part-7.crc
new file mode 100644
index 0000000..f7bdcc6
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/.part-7.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/part-0 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/part-0
new file mode 100755
index 0000000..d48bb3c
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/part-0
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/part-1 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/part-1
new file mode 100755
index 0000000..4208d9c
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/part-1
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/part-2 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/part-2
new file mode 100755
index 0000000..1cb547b
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/part-2
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/part-3 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/part-3
new file mode 100755
index 0000000..4a572b8
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/part-3
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/part-4 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/part-4
new file mode 100755
index 0000000..02a769e
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/part-4
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/part-5 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/part-5
new file mode 100755
index 0000000..ba66f5d
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/part-5
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/part-6 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/part-6
new file mode 100755
index 0000000..e024df1
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/part-6
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/part-7 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/part-7
new file mode 100755
index 0000000..a38291e
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/bin/part-7
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/graphviz/result.ps b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/graphviz/result.ps
new file mode 100644
index 0000000..a8e6c9a
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/graphviz/result.ps
@@ -0,0 +1,581 @@
+%!PS-Adobe-3.0
+%%Creator: graphviz version 2.26.3 (20100126.1600)
+%%Title: G
+%%Pages: (atend)
+%%BoundingBox: (atend)
+%%EndComments
+save
+%%BeginProlog
+/DotDict 200 dict def
+DotDict begin
+
+/setupLatin1 {
+mark
+/EncodingVector 256 array def
+ EncodingVector 0
+
+ISOLatin1Encoding 0 255 getinterval putinterval
+EncodingVector 45 /hyphen put
+
+% Set up ISO Latin 1 character encoding
+/starnetISO {
+ dup dup findfont dup length dict begin
+ { 1 index /FID ne { def }{ pop pop } ifelse
+ } forall
+ /Encoding EncodingVector def
+ currentdict end definefont
+} def
+/Times-Roman starnetISO def
+/Times-Italic starnetISO def
+/Times-Bold starnetISO def
+/Times-BoldItalic starnetISO def
+/Helvetica starnetISO def
+/Helvetica-Oblique starnetISO def
+/Helvetica-Bold starnetISO def
+/Helvetica-BoldOblique starnetISO def
+/Courier starnetISO def
+/Courier-Oblique starnetISO def
+/Courier-Bold starnetISO def
+/Courier-BoldOblique starnetISO def
+cleartomark
+} bind def
+
+%%BeginResource: procset graphviz 0 0
+/coord-font-family /Times-Roman def
+/default-font-family /Times-Roman def
+/coordfont coord-font-family findfont 8 scalefont def
+
+/InvScaleFactor 1.0 def
+/set_scale {
+ dup 1 exch div /InvScaleFactor exch def
+ scale
+} bind def
+
+% styles
+/solid { [] 0 setdash } bind def
+/dashed { [9 InvScaleFactor mul dup ] 0 setdash } bind def
+/dotted { [1 InvScaleFactor mul 6 InvScaleFactor mul] 0 setdash } bind def
+/invis {/fill {newpath} def /stroke {newpath} def /show {pop newpath} def} bind def
+/bold { 2 setlinewidth } bind def
+/filled { } bind def
+/unfilled { } bind def
+/rounded { } bind def
+/diagonals { } bind def
+
+% hooks for setting color
+/nodecolor { sethsbcolor } bind def
+/edgecolor { sethsbcolor } bind def
+/graphcolor { sethsbcolor } bind def
+/nopcolor {pop pop pop} bind def
+
+/beginpage { % i j npages
+ /npages exch def
+ /j exch def
+ /i exch def
+ /str 10 string def
+ npages 1 gt {
+ gsave
+ coordfont setfont
+ 0 0 moveto
+ (\() show i str cvs show (,) show j str cvs show (\)) show
+ grestore
+ } if
+} bind def
+
+/set_font {
+ findfont exch
+ scalefont setfont
+} def
+
+% draw text fitted to its expected width
+/alignedtext { % width text
+ /text exch def
+ /width exch def
+ gsave
+ width 0 gt {
+ [] 0 setdash
+ text stringwidth pop width exch sub text length div 0 text ashow
+ } if
+ grestore
+} def
+
+/boxprim { % xcorner ycorner xsize ysize
+ 4 2 roll
+ moveto
+ 2 copy
+ exch 0 rlineto
+ 0 exch rlineto
+ pop neg 0 rlineto
+ closepath
+} bind def
+
+/ellipse_path {
+ /ry exch def
+ /rx exch def
+ /y exch def
+ /x exch def
+ matrix currentmatrix
+ newpath
+ x y translate
+ rx ry scale
+ 0 0 1 0 360 arc
+ setmatrix
+} bind def
+
+/endpage { showpage } bind def
+/showpage { } def
+
+/layercolorseq
+ [ % layer color sequence - darkest to lightest
+ [0 0 0]
+ [.2 .8 .8]
+ [.4 .8 .8]
+ [.6 .8 .8]
+ [.8 .8 .8]
+ ]
+def
+
+/layerlen layercolorseq length def
+
+/setlayer {/maxlayer exch def /curlayer exch def
+ layercolorseq curlayer 1 sub layerlen mod get
+ aload pop sethsbcolor
+ /nodecolor {nopcolor} def
+ /edgecolor {nopcolor} def
+ /graphcolor {nopcolor} def
+} bind def
+
+/onlayer { curlayer ne {invis} if } def
+
+/onlayers {
+ /myupper exch def
+ /mylower exch def
+ curlayer mylower lt
+ curlayer myupper gt
+ or
+ {invis} if
+} def
+
+/curlayer 0 def
+
+%%EndResource
+%%EndProlog
+%%BeginSetup
+14 default-font-family set_font
+1 setmiterlimit
+% /arrowlength 10 def
+% /arrowwidth 5 def
+
+% make sure pdfmark is harmless for PS-interpreters other than Distiller
+/pdfmark where {pop} {userdict /pdfmark /cleartomark load put} ifelse
+% make '<<' and '>>' safe on PS Level 1 devices
+/languagelevel where {pop languagelevel}{1} ifelse
+2 lt {
+ userdict (<<) cvn ([) cvn load put
+ userdict (>>) cvn ([) cvn load put
+} if
+
+%%EndSetup
+setupLatin1
+%%Page: 1 1
+%%PageBoundingBox: 36 36 606 248
+%%PageOrientation: Portrait
+0 0 1 beginpage
+gsave
+36 36 570 212 boxprim clip newpath
+1 1 set_scale 0 rotate 40 41 translate
+% GGA
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 0 moveto
+0 130 lineto
+56 130 lineto
+56 0 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+11.5 113.4 moveto 33 (GGA) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 104 moveto
+56 104 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+14 87.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 78 moveto
+56 78 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+8 61.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 52 moveto
+56 52 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+16.5 35.4 moveto 23 (2.0) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 26 moveto
+56 26 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+11.5 9.4 moveto 33 (GGA) alignedtext
+grestore
+% CCG
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 138 74 moveto
+138 204 lineto
+226 204 lineto
+226 74 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+166.5 187.4 moveto 31 (CCG) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 138 178 moveto
+226 178 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+168 161.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 138 152 moveto
+226 152 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+162 135.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 138 126 moveto
+226 126 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+170.5 109.4 moveto 23 (1.0) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 138 100 moveto
+226 100 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+146 83.4 moveto 72 (CCAGCCG) alignedtext
+grestore
+% GGA->CCG
+gsave
+1 setlinewidth
+0.33333 1 1 edgecolor
+newpath 56.23 93.51 moveto
+61.81 98.14 67.85 102.54 74 106 curveto
+90.65 115.37 110.28 122.38 128.2 127.48 curveto
+stroke
+0.33333 1 1 edgecolor
+newpath 127.38 130.89 moveto
+137.95 130.12 lineto
+129.21 124.13 lineto
+closepath fill
+1 setlinewidth
+solid
+0.33333 1 1 edgecolor
+newpath 127.38 130.89 moveto
+137.95 130.12 lineto
+129.21 124.13 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+74 129.4 moveto 46 (RF: [2]) alignedtext
+grestore
+% AGG
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 470.5 2 moveto
+470.5 132 lineto
+561.5 132 lineto
+561.5 2 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+499.5 115.4 moveto 33 (AGG) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 470.5 106 moveto
+561.5 106 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+502 89.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 470.5 80 moveto
+561.5 80 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+496 63.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 470.5 54 moveto
+561.5 54 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+504.5 37.4 moveto 23 (1.0) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 470.5 28 moveto
+561.5 28 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+478.5 11.4 moveto 75 (CGAAAGG) alignedtext
+grestore
+% GGA->AGG
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 56.01 64.85 moveto
+116.57 64.56 264.25 64.03 388 65 curveto
+411.71 65.19 437.88 65.56 460.35 65.94 curveto
+stroke
+0 1 1 edgecolor
+newpath 460.33 69.44 moveto
+470.39 66.11 lineto
+460.45 62.44 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 460.33 69.44 moveto
+470.39 66.11 lineto
+460.45 62.44 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+244 69.4 moveto 48 (RR: [1]) alignedtext
+grestore
+% CCG->GGA
+gsave
+1 setlinewidth
+0.33333 1 1 edgecolor
+newpath 137.95 95.21 moveto
+132.21 90.96 126.17 87.09 120 84 curveto
+103.46 75.71 83.51 71.03 66.42 68.4 curveto
+stroke
+0.33333 1 1 edgecolor
+newpath 66.59 64.89 moveto
+56.21 67.01 lineto
+65.64 71.83 lineto
+closepath fill
+1 setlinewidth
+solid
+0.33333 1 1 edgecolor
+newpath 66.59 64.89 moveto
+56.21 67.01 lineto
+65.64 71.83 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+74 89.4 moveto 46 (RF: [2]) alignedtext
+grestore
+% CGC
+gsave
+0 0 0.75294 nodecolor
+newpath 310 74 moveto
+310 204 lineto
+388 204 lineto
+388 74 lineto
+closepath fill
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 310 74 moveto
+310 204 lineto
+388 204 lineto
+388 74 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+333.5 187.4 moveto 31 (CGC) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 310 178 moveto
+388 178 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+335 161.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 310 152 moveto
+388 152 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+318 135.4 moveto 62 (~5':[2,1]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 310 126 moveto
+388 126 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+337.5 109.4 moveto 23 (2.0) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 310 100 moveto
+388 100 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+333.5 83.4 moveto 31 (CGC) alignedtext
+grestore
+% CCG->CGC
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 226.31 139 moveto
+248.96 139 276.57 139 299.86 139 curveto
+stroke
+0 0 0 edgecolor
+newpath 299.89 142.5 moveto
+309.89 139 lineto
+299.89 135.5 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 299.89 142.5 moveto
+309.89 139 lineto
+299.89 135.5 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+245.5 144.4 moveto 45 (FF: [2]) alignedtext
+grestore
+% AGG->GGA
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 470.22 60.38 moveto
+425.04 54.21 353.93 45.44 292 42 curveto
+194.93 36.6 170.66 49.63 74 60 curveto
+71.48 60.27 68.89 60.55 66.28 60.83 curveto
+stroke
+0 0 0 edgecolor
+newpath 65.78 57.36 moveto
+56.22 61.92 lineto
+66.54 64.32 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 65.78 57.36 moveto
+56.22 61.92 lineto
+66.54 64.32 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+245.5 47.4 moveto 45 (FF: [1]) alignedtext
+grestore
+% AGG->CGC
+gsave
+1 setlinewidth
+0.33333 1 1 edgecolor
+newpath 470.35 70.15 moveto
+449.85 72.94 425.87 78.17 406 88 curveto
+402.71 89.63 399.47 91.5 396.3 93.54 curveto
+stroke
+0.33333 1 1 edgecolor
+newpath 394.28 90.68 moveto
+388.11 99.29 lineto
+398.3 96.41 lineto
+closepath fill
+1 setlinewidth
+solid
+0.33333 1 1 edgecolor
+newpath 394.28 90.68 moveto
+388.11 99.29 lineto
+398.3 96.41 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+406 93.4 moveto 46 (RF: [1]) alignedtext
+grestore
+% CGC->CCG
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 309.99 121.79 moveto
+304.07 119.81 297.94 118.11 292 117 curveto
+271.03 113.09 265.02 113.38 244 117 curveto
+241.35 117.46 238.66 118.02 235.96 118.65 curveto
+stroke
+0 1 1 edgecolor
+newpath 234.96 115.3 moveto
+226.21 121.27 lineto
+236.78 122.06 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 234.96 115.3 moveto
+226.21 121.27 lineto
+236.78 122.06 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+244 122.4 moveto 48 (RR: [2]) alignedtext
+grestore
+% CGC->AGG
+gsave
+1 setlinewidth
+0.33333 1 1 edgecolor
+newpath 388.19 131.06 moveto
+407.87 126.31 431.76 119.35 452 110 curveto
+455.13 108.55 458.28 106.96 461.42 105.27 curveto
+stroke
+0.33333 1 1 edgecolor
+newpath 463.23 108.26 moveto
+470.17 100.26 lineto
+459.75 102.19 lineto
+closepath fill
+1 setlinewidth
+solid
+0.33333 1 1 edgecolor
+newpath 463.23 108.26 moveto
+470.17 100.26 lineto
+459.75 102.19 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+406 130.4 moveto 46 (RF: [1]) alignedtext
+grestore
+endpage
+showpage
+grestore
+%%PageTrailer
+%%EndPage: 1
+%%Trailer
+%%Pages: 1
+%%BoundingBox: 36 36 606 248
+end
+restore
+%%EOF
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/txt b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/txt
new file mode 100755
index 0000000..94ba66b
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoL/txt
@@ -0,0 +1,4 @@
+GGA {[] [] [{CCG:[2]}] [{AGG:[1]}] {5':[], ~5':[]}GGA 2.0x}
+CCG {[{CGC:[2]}] [] [{GGA:[2]}] [] {5':[], ~5':[]}CCAGCCG 1.0x}
+CGC {[] [] [{AGG:[1]}] [{CCG:[2]}] {5':[], ~5':[(2-0_0),(1-0_0)]}CGC 2.0x}
+AGG {[{GGA:[1]}] [] [{CGC:[1]}] [] {5':[], ~5':[]}CGAAAGG 1.0x}
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/.txt.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/.txt.crc
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/.txt.crc
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/.part-0.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/.part-0.crc
new file mode 100644
index 0000000..5237ad0
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/.part-0.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/.part-1.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/.part-1.crc
new file mode 100644
index 0000000..8824f53
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/.part-1.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/.part-2.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/.part-2.crc
new file mode 100644
index 0000000..468f683
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/.part-2.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/.part-3.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/.part-3.crc
new file mode 100644
index 0000000..7de88c7
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/.part-3.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/.part-4.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/.part-4.crc
new file mode 100644
index 0000000..4f18f60
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/.part-4.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/.part-5.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/.part-5.crc
new file mode 100644
index 0000000..ba8c7eb
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/.part-5.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/.part-6.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/.part-6.crc
new file mode 100644
index 0000000..38c6c0d
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/.part-6.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/.part-7.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/.part-7.crc
new file mode 100644
index 0000000..ef023c0
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/.part-7.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/part-0 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/part-0
new file mode 100755
index 0000000..78e797b
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/part-0
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/part-1 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/part-1
new file mode 100755
index 0000000..52d54f9
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/part-1
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/part-2 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/part-2
new file mode 100755
index 0000000..79d6192
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/part-2
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/part-3 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/part-3
new file mode 100755
index 0000000..b682b93
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/part-3
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/part-4 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/part-4
new file mode 100755
index 0000000..d36b069
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/part-4
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/part-5 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/part-5
new file mode 100755
index 0000000..e06f1f9
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/part-5
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/part-6 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/part-6
new file mode 100755
index 0000000..a8079f9
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/part-6
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/part-7 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/part-7
new file mode 100755
index 0000000..f101ae4
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/bin/part-7
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/graphviz/result.ps b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/graphviz/result.ps
new file mode 100644
index 0000000..11bfb59
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/graphviz/result.ps
@@ -0,0 +1,581 @@
+%!PS-Adobe-3.0
+%%Creator: graphviz version 2.26.3 (20100126.1600)
+%%Title: G
+%%Pages: (atend)
+%%BoundingBox: (atend)
+%%EndComments
+save
+%%BeginProlog
+/DotDict 200 dict def
+DotDict begin
+
+/setupLatin1 {
+mark
+/EncodingVector 256 array def
+ EncodingVector 0
+
+ISOLatin1Encoding 0 255 getinterval putinterval
+EncodingVector 45 /hyphen put
+
+% Set up ISO Latin 1 character encoding
+/starnetISO {
+ dup dup findfont dup length dict begin
+ { 1 index /FID ne { def }{ pop pop } ifelse
+ } forall
+ /Encoding EncodingVector def
+ currentdict end definefont
+} def
+/Times-Roman starnetISO def
+/Times-Italic starnetISO def
+/Times-Bold starnetISO def
+/Times-BoldItalic starnetISO def
+/Helvetica starnetISO def
+/Helvetica-Oblique starnetISO def
+/Helvetica-Bold starnetISO def
+/Helvetica-BoldOblique starnetISO def
+/Courier starnetISO def
+/Courier-Oblique starnetISO def
+/Courier-Bold starnetISO def
+/Courier-BoldOblique starnetISO def
+cleartomark
+} bind def
+
+%%BeginResource: procset graphviz 0 0
+/coord-font-family /Times-Roman def
+/default-font-family /Times-Roman def
+/coordfont coord-font-family findfont 8 scalefont def
+
+/InvScaleFactor 1.0 def
+/set_scale {
+ dup 1 exch div /InvScaleFactor exch def
+ scale
+} bind def
+
+% styles
+/solid { [] 0 setdash } bind def
+/dashed { [9 InvScaleFactor mul dup ] 0 setdash } bind def
+/dotted { [1 InvScaleFactor mul 6 InvScaleFactor mul] 0 setdash } bind def
+/invis {/fill {newpath} def /stroke {newpath} def /show {pop newpath} def} bind def
+/bold { 2 setlinewidth } bind def
+/filled { } bind def
+/unfilled { } bind def
+/rounded { } bind def
+/diagonals { } bind def
+
+% hooks for setting color
+/nodecolor { sethsbcolor } bind def
+/edgecolor { sethsbcolor } bind def
+/graphcolor { sethsbcolor } bind def
+/nopcolor {pop pop pop} bind def
+
+/beginpage { % i j npages
+ /npages exch def
+ /j exch def
+ /i exch def
+ /str 10 string def
+ npages 1 gt {
+ gsave
+ coordfont setfont
+ 0 0 moveto
+ (\() show i str cvs show (,) show j str cvs show (\)) show
+ grestore
+ } if
+} bind def
+
+/set_font {
+ findfont exch
+ scalefont setfont
+} def
+
+% draw text fitted to its expected width
+/alignedtext { % width text
+ /text exch def
+ /width exch def
+ gsave
+ width 0 gt {
+ [] 0 setdash
+ text stringwidth pop width exch sub text length div 0 text ashow
+ } if
+ grestore
+} def
+
+/boxprim { % xcorner ycorner xsize ysize
+ 4 2 roll
+ moveto
+ 2 copy
+ exch 0 rlineto
+ 0 exch rlineto
+ pop neg 0 rlineto
+ closepath
+} bind def
+
+/ellipse_path {
+ /ry exch def
+ /rx exch def
+ /y exch def
+ /x exch def
+ matrix currentmatrix
+ newpath
+ x y translate
+ rx ry scale
+ 0 0 1 0 360 arc
+ setmatrix
+} bind def
+
+/endpage { showpage } bind def
+/showpage { } def
+
+/layercolorseq
+ [ % layer color sequence - darkest to lightest
+ [0 0 0]
+ [.2 .8 .8]
+ [.4 .8 .8]
+ [.6 .8 .8]
+ [.8 .8 .8]
+ ]
+def
+
+/layerlen layercolorseq length def
+
+/setlayer {/maxlayer exch def /curlayer exch def
+ layercolorseq curlayer 1 sub layerlen mod get
+ aload pop sethsbcolor
+ /nodecolor {nopcolor} def
+ /edgecolor {nopcolor} def
+ /graphcolor {nopcolor} def
+} bind def
+
+/onlayer { curlayer ne {invis} if } def
+
+/onlayers {
+ /myupper exch def
+ /mylower exch def
+ curlayer mylower lt
+ curlayer myupper gt
+ or
+ {invis} if
+} def
+
+/curlayer 0 def
+
+%%EndResource
+%%EndProlog
+%%BeginSetup
+14 default-font-family set_font
+1 setmiterlimit
+% /arrowlength 10 def
+% /arrowwidth 5 def
+
+% make sure pdfmark is harmless for PS-interpreters other than Distiller
+/pdfmark where {pop} {userdict /pdfmark /cleartomark load put} ifelse
+% make '<<' and '>>' safe on PS Level 1 devices
+/languagelevel where {pop languagelevel}{1} ifelse
+2 lt {
+ userdict (<<) cvn ([) cvn load put
+ userdict (>>) cvn ([) cvn load put
+} if
+
+%%EndSetup
+setupLatin1
+%%Page: 1 1
+%%PageBoundingBox: 36 36 608 248
+%%PageOrientation: Portrait
+0 0 1 beginpage
+gsave
+36 36 572 212 boxprim clip newpath
+1 1 set_scale 0 rotate 40 41 translate
+% ACC
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 0 moveto
+0 130 lineto
+56 130 lineto
+56 0 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+13 113.4 moveto 30 (ACC) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 104 moveto
+56 104 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+14 87.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 78 moveto
+56 78 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+8 61.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 52 moveto
+56 52 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+16.5 35.4 moveto 23 (2.0) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 26 moveto
+56 26 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+13 9.4 moveto 30 (ACC) alignedtext
+grestore
+% CCG
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 140 74 moveto
+140 204 lineto
+228 204 lineto
+228 74 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+168.5 187.4 moveto 31 (CCG) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 140 178 moveto
+228 178 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+170 161.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 140 152 moveto
+228 152 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+164 135.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 140 126 moveto
+228 126 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+172.5 109.4 moveto 23 (1.0) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 140 100 moveto
+228 100 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+148 83.4 moveto 72 (CCAGCCG) alignedtext
+grestore
+% ACC->CCG
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 56.22 93.54 moveto
+61.79 98.16 67.84 102.55 74 106 curveto
+91.26 115.65 111.66 122.77 130.17 127.88 curveto
+stroke
+0 0 0 edgecolor
+newpath 129.38 131.29 moveto
+139.94 130.45 lineto
+131.15 124.52 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 129.38 131.29 moveto
+139.94 130.45 lineto
+131.15 124.52 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+75.5 130.4 moveto 45 (FF: [2]) alignedtext
+grestore
+% AGG
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 472.5 2 moveto
+472.5 132 lineto
+563.5 132 lineto
+563.5 2 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+501.5 115.4 moveto 33 (AGG) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 472.5 106 moveto
+563.5 106 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+504 89.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 472.5 80 moveto
+563.5 80 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+498 63.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 472.5 54 moveto
+563.5 54 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+506.5 37.4 moveto 23 (1.0) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 472.5 28 moveto
+563.5 28 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+480.5 11.4 moveto 75 (CGAAAGG) alignedtext
+grestore
+% ACC->AGG
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 56.16 64.85 moveto
+117.07 64.56 265.57 64.03 390 65 curveto
+413.71 65.19 439.88 65.56 462.35 65.94 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 462.33 69.44 moveto
+472.39 66.11 lineto
+462.45 62.44 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 462.33 69.44 moveto
+472.39 66.11 lineto
+462.45 62.44 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+247 69.4 moveto 46 (FR: [1]) alignedtext
+grestore
+% CCG->ACC
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 139.96 95.18 moveto
+134.22 90.94 128.18 87.08 122 84 curveto
+104.81 75.43 84.03 70.72 66.38 68.14 curveto
+stroke
+0 1 1 edgecolor
+newpath 66.76 64.66 moveto
+56.4 66.85 lineto
+65.87 71.61 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 66.76 64.66 moveto
+56.4 66.85 lineto
+65.87 71.61 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+74 89.4 moveto 48 (RR: [2]) alignedtext
+grestore
+% CGC
+gsave
+0 0 0.75294 nodecolor
+newpath 312 74 moveto
+312 204 lineto
+390 204 lineto
+390 74 lineto
+closepath fill
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 312 74 moveto
+312 204 lineto
+390 204 lineto
+390 74 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+335.5 187.4 moveto 31 (CGC) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 312 178 moveto
+390 178 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+337 161.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 312 152 moveto
+390 152 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+320 135.4 moveto 62 (~5':[2,1]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 312 126 moveto
+390 126 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+339.5 109.4 moveto 23 (2.0) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 312 100 moveto
+390 100 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+335.5 83.4 moveto 31 (CGC) alignedtext
+grestore
+% CCG->CGC
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 228.31 139 moveto
+250.96 139 278.57 139 301.86 139 curveto
+stroke
+0 0 0 edgecolor
+newpath 301.89 142.5 moveto
+311.89 139 lineto
+301.89 135.5 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 301.89 142.5 moveto
+311.89 139 lineto
+301.89 135.5 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+247.5 144.4 moveto 45 (FF: [2]) alignedtext
+grestore
+% AGG->ACC
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 472.22 60.38 moveto
+427.04 54.21 355.93 45.44 294 42 curveto
+196.05 36.55 171.55 49.59 74 60 curveto
+71.48 60.27 68.89 60.55 66.28 60.83 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 65.78 57.36 moveto
+56.22 61.91 lineto
+66.54 64.32 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 65.78 57.36 moveto
+56.22 61.91 lineto
+66.54 64.32 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+247 47.4 moveto 46 (FR: [1]) alignedtext
+grestore
+% AGG->CGC
+gsave
+1 setlinewidth
+0.33333 1 1 edgecolor
+newpath 472.35 70.15 moveto
+451.85 72.94 427.87 78.17 408 88 curveto
+404.71 89.63 401.47 91.5 398.3 93.54 curveto
+stroke
+0.33333 1 1 edgecolor
+newpath 396.28 90.68 moveto
+390.11 99.29 lineto
+400.3 96.41 lineto
+closepath fill
+1 setlinewidth
+solid
+0.33333 1 1 edgecolor
+newpath 396.28 90.68 moveto
+390.11 99.29 lineto
+400.3 96.41 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+408 93.4 moveto 46 (RF: [1]) alignedtext
+grestore
+% CGC->CCG
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 311.99 121.79 moveto
+306.07 119.81 299.94 118.11 294 117 curveto
+273.03 113.09 267.02 113.38 246 117 curveto
+243.35 117.46 240.66 118.02 237.96 118.65 curveto
+stroke
+0 1 1 edgecolor
+newpath 236.96 115.3 moveto
+228.21 121.27 lineto
+238.78 122.06 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 236.96 115.3 moveto
+228.21 121.27 lineto
+238.78 122.06 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+246 122.4 moveto 48 (RR: [2]) alignedtext
+grestore
+% CGC->AGG
+gsave
+1 setlinewidth
+0.33333 1 1 edgecolor
+newpath 390.19 131.06 moveto
+409.87 126.31 433.76 119.35 454 110 curveto
+457.13 108.55 460.28 106.96 463.42 105.27 curveto
+stroke
+0.33333 1 1 edgecolor
+newpath 465.23 108.26 moveto
+472.17 100.26 lineto
+461.75 102.19 lineto
+closepath fill
+1 setlinewidth
+solid
+0.33333 1 1 edgecolor
+newpath 465.23 108.26 moveto
+472.17 100.26 lineto
+461.75 102.19 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+408 130.4 moveto 46 (RF: [1]) alignedtext
+grestore
+endpage
+showpage
+grestore
+%%PageTrailer
+%%EndPage: 1
+%%Trailer
+%%Pages: 1
+%%BoundingBox: 36 36 608 248
+end
+restore
+%%EOF
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/txt b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/txt
new file mode 100755
index 0000000..e827ac6
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/RtoR/txt
@@ -0,0 +1,4 @@
+ACC {[{CCG:[2]}] [{AGG:[1]}] [] [] {5':[], ~5':[]}ACC 2.0x}
+CCG {[{CGC:[2]}] [] [] [{ACC:[2]}] {5':[], ~5':[]}CCAGCCG 1.0x}
+CGC {[] [] [{AGG:[1]}] [{CCG:[2]}] {5':[], ~5':[(2-0_0),(1-0_0)]}CGC 2.0x}
+AGG {[] [{ACC:[1]}] [{CGC:[1]}] [] {5':[], ~5':[]}CGAAAGG 1.0x}
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/.txt.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/.txt.crc
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/.txt.crc
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/.part-0.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/.part-0.crc
new file mode 100644
index 0000000..c51adb4
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/.part-0.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/.part-1.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/.part-1.crc
new file mode 100644
index 0000000..f7706ab
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/.part-1.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/.part-2.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/.part-2.crc
new file mode 100644
index 0000000..06c807e
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/.part-2.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/.part-3.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/.part-3.crc
new file mode 100644
index 0000000..b46c964
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/.part-3.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/.part-4.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/.part-4.crc
new file mode 100644
index 0000000..76705dd
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/.part-4.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/.part-5.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/.part-5.crc
new file mode 100644
index 0000000..492d091
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/.part-5.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/.part-6.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/.part-6.crc
new file mode 100644
index 0000000..95e19d4
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/.part-6.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/.part-7.crc b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/.part-7.crc
new file mode 100644
index 0000000..4dc3ae7
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/.part-7.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/part-0 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/part-0
new file mode 100755
index 0000000..b3721e0
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/part-0
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/part-1 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/part-1
new file mode 100755
index 0000000..7f0ea63
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/part-1
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/part-2 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/part-2
new file mode 100755
index 0000000..18aeaf6
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/part-2
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/part-3 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/part-3
new file mode 100755
index 0000000..a3a8907
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/part-3
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/part-4 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/part-4
new file mode 100755
index 0000000..0ee4541
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/part-4
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/part-5 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/part-5
new file mode 100755
index 0000000..542bde2
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/part-5
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/part-6 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/part-6
new file mode 100755
index 0000000..0e9a6a5
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/part-6
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/part-7 b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/part-7
new file mode 100755
index 0000000..abf788a
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/bin/part-7
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/graphviz/result.ps b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/graphviz/result.ps
new file mode 100644
index 0000000..7f5955e
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/graphviz/result.ps
@@ -0,0 +1,583 @@
+%!PS-Adobe-3.0
+%%Creator: graphviz version 2.26.3 (20100126.1600)
+%%Title: G
+%%Pages: (atend)
+%%BoundingBox: (atend)
+%%EndComments
+save
+%%BeginProlog
+/DotDict 200 dict def
+DotDict begin
+
+/setupLatin1 {
+mark
+/EncodingVector 256 array def
+ EncodingVector 0
+
+ISOLatin1Encoding 0 255 getinterval putinterval
+EncodingVector 45 /hyphen put
+
+% Set up ISO Latin 1 character encoding
+/starnetISO {
+ dup dup findfont dup length dict begin
+ { 1 index /FID ne { def }{ pop pop } ifelse
+ } forall
+ /Encoding EncodingVector def
+ currentdict end definefont
+} def
+/Times-Roman starnetISO def
+/Times-Italic starnetISO def
+/Times-Bold starnetISO def
+/Times-BoldItalic starnetISO def
+/Helvetica starnetISO def
+/Helvetica-Oblique starnetISO def
+/Helvetica-Bold starnetISO def
+/Helvetica-BoldOblique starnetISO def
+/Courier starnetISO def
+/Courier-Oblique starnetISO def
+/Courier-Bold starnetISO def
+/Courier-BoldOblique starnetISO def
+cleartomark
+} bind def
+
+%%BeginResource: procset graphviz 0 0
+/coord-font-family /Times-Roman def
+/default-font-family /Times-Roman def
+/coordfont coord-font-family findfont 8 scalefont def
+
+/InvScaleFactor 1.0 def
+/set_scale {
+ dup 1 exch div /InvScaleFactor exch def
+ scale
+} bind def
+
+% styles
+/solid { [] 0 setdash } bind def
+/dashed { [9 InvScaleFactor mul dup ] 0 setdash } bind def
+/dotted { [1 InvScaleFactor mul 6 InvScaleFactor mul] 0 setdash } bind def
+/invis {/fill {newpath} def /stroke {newpath} def /show {pop newpath} def} bind def
+/bold { 2 setlinewidth } bind def
+/filled { } bind def
+/unfilled { } bind def
+/rounded { } bind def
+/diagonals { } bind def
+
+% hooks for setting color
+/nodecolor { sethsbcolor } bind def
+/edgecolor { sethsbcolor } bind def
+/graphcolor { sethsbcolor } bind def
+/nopcolor {pop pop pop} bind def
+
+/beginpage { % i j npages
+ /npages exch def
+ /j exch def
+ /i exch def
+ /str 10 string def
+ npages 1 gt {
+ gsave
+ coordfont setfont
+ 0 0 moveto
+ (\() show i str cvs show (,) show j str cvs show (\)) show
+ grestore
+ } if
+} bind def
+
+/set_font {
+ findfont exch
+ scalefont setfont
+} def
+
+% draw text fitted to its expected width
+/alignedtext { % width text
+ /text exch def
+ /width exch def
+ gsave
+ width 0 gt {
+ [] 0 setdash
+ text stringwidth pop width exch sub text length div 0 text ashow
+ } if
+ grestore
+} def
+
+/boxprim { % xcorner ycorner xsize ysize
+ 4 2 roll
+ moveto
+ 2 copy
+ exch 0 rlineto
+ 0 exch rlineto
+ pop neg 0 rlineto
+ closepath
+} bind def
+
+/ellipse_path {
+ /ry exch def
+ /rx exch def
+ /y exch def
+ /x exch def
+ matrix currentmatrix
+ newpath
+ x y translate
+ rx ry scale
+ 0 0 1 0 360 arc
+ setmatrix
+} bind def
+
+/endpage { showpage } bind def
+/showpage { } def
+
+/layercolorseq
+ [ % layer color sequence - darkest to lightest
+ [0 0 0]
+ [.2 .8 .8]
+ [.4 .8 .8]
+ [.6 .8 .8]
+ [.8 .8 .8]
+ ]
+def
+
+/layerlen layercolorseq length def
+
+/setlayer {/maxlayer exch def /curlayer exch def
+ layercolorseq curlayer 1 sub layerlen mod get
+ aload pop sethsbcolor
+ /nodecolor {nopcolor} def
+ /edgecolor {nopcolor} def
+ /graphcolor {nopcolor} def
+} bind def
+
+/onlayer { curlayer ne {invis} if } def
+
+/onlayers {
+ /myupper exch def
+ /mylower exch def
+ curlayer mylower lt
+ curlayer myupper gt
+ or
+ {invis} if
+} def
+
+/curlayer 0 def
+
+%%EndResource
+%%EndProlog
+%%BeginSetup
+14 default-font-family set_font
+1 setmiterlimit
+% /arrowlength 10 def
+% /arrowwidth 5 def
+
+% make sure pdfmark is harmless for PS-interpreters other than Distiller
+/pdfmark where {pop} {userdict /pdfmark /cleartomark load put} ifelse
+% make '<<' and '>>' safe on PS Level 1 devices
+/languagelevel where {pop languagelevel}{1} ifelse
+2 lt {
+ userdict (<<) cvn ([) cvn load put
+ userdict (>>) cvn ([) cvn load put
+} if
+
+%%EndSetup
+setupLatin1
+%%Page: 1 1
+%%PageBoundingBox: 36 36 554 248
+%%PageOrientation: Portrait
+0 0 1 beginpage
+gsave
+36 36 518 212 boxprim clip newpath
+1 1 set_scale 0 rotate 40 41 translate
+% TAA
+gsave
+0 0 0.75294 nodecolor
+newpath 0 0 moveto
+0 130 lineto
+66 130 lineto
+66 0 lineto
+closepath fill
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 0 0 moveto
+0 130 lineto
+66 130 lineto
+66 0 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+18.5 113.4 moveto 29 (TAA) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 0 104 moveto
+66 104 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+8 87.4 moveto 50 (5':[2,1]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 0 78 moveto
+66 78 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+13 61.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 0 52 moveto
+66 52 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+21.5 35.4 moveto 23 (2.0) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 0 26 moveto
+66 26 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+18.5 9.4 moveto 29 (TAA) alignedtext
+grestore
+% AAC
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 150.5 74 moveto
+150.5 204 lineto
+217.5 204 lineto
+217.5 74 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+168.5 187.4 moveto 31 (AAC) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 150.5 178 moveto
+217.5 178 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+170 161.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 150.5 152 moveto
+217.5 152 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+164 135.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 150.5 126 moveto
+217.5 126 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+172.5 109.4 moveto 23 (1.0) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 150.5 100 moveto
+217.5 100 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+158.5 83.4 moveto 51 (AACAA) alignedtext
+grestore
+% TAA->AAC
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 66.1 94.36 moveto
+71.83 98.63 77.91 102.69 84 106 curveto
+101.62 115.58 122.5 123.01 140.61 128.37 curveto
+stroke
+0 0 0 edgecolor
+newpath 139.77 131.77 moveto
+150.35 131.14 lineto
+141.68 125.04 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 139.77 131.77 moveto
+150.35 131.14 lineto
+141.68 125.04 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+85.5 130.4 moveto 45 (FF: [1]) alignedtext
+grestore
+% AGA
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 442 2 moveto
+442 132 lineto
+510 132 lineto
+510 2 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+460.5 115.4 moveto 31 (AGA) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 442 106 moveto
+510 106 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+462 89.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 442 80 moveto
+510 80 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+456 63.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 442 54 moveto
+510 54 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+464.5 37.4 moveto 23 (1.0) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 442 28 moveto
+510 28 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+450 11.4 moveto 52 (AAGAA) alignedtext
+grestore
+% TAA->AGA
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 66.19 64.25 moveto
+72.12 64.15 78.24 64.06 84 64 curveto
+105.33 63.79 110.67 63.95 132 64 curveto
+232.45 64.22 257.56 63.93 358 65 curveto
+382.41 65.26 409.65 65.71 431.81 66.12 curveto
+stroke
+0 0 0 edgecolor
+newpath 431.86 69.62 moveto
+441.92 66.31 lineto
+431.99 62.62 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 431.86 69.62 moveto
+441.92 66.31 lineto
+431.99 62.62 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+237.5 69.4 moveto 45 (FF: [2]) alignedtext
+grestore
+% AAC->TAA
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 150.49 97.49 moveto
+144.79 92.33 138.57 87.6 132 84 curveto
+115.12 74.74 94.46 69.93 76.39 67.46 curveto
+stroke
+0 1 1 edgecolor
+newpath 76.72 63.97 moveto
+66.38 66.28 lineto
+75.9 70.93 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 76.72 63.97 moveto
+66.38 66.28 lineto
+75.9 70.93 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+84 89.4 moveto 48 (RR: [1]) alignedtext
+grestore
+% AAA
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 302 74 moveto
+302 204 lineto
+358 204 lineto
+358 74 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+314.5 187.4 moveto 31 (AAA) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 302 178 moveto
+358 178 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+316 161.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 302 152 moveto
+358 152 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+310 135.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 302 126 moveto
+358 126 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+318.5 109.4 moveto 23 (2.0) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 302 100 moveto
+358 100 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+314.5 83.4 moveto 31 (AAA) alignedtext
+grestore
+% AAC->AAA
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 217.86 139 moveto
+239.92 139 268.76 139 291.66 139 curveto
+stroke
+0 0 0 edgecolor
+newpath 291.72 142.5 moveto
+301.72 139 lineto
+291.72 135.5 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 291.72 142.5 moveto
+301.72 139 lineto
+291.72 135.5 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+237.5 144.4 moveto 45 (FF: [1]) alignedtext
+grestore
+% AGA->TAA
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 441.79 61.19 moveto
+403.5 54.99 339.52 45.6 284 42 curveto
+194.98 36.23 172.63 48.83 84 59 curveto
+81.48 59.29 78.89 59.59 76.28 59.89 curveto
+stroke
+0 1 1 edgecolor
+newpath 75.72 56.43 moveto
+66.19 61.07 lineto
+76.53 63.39 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 75.72 56.43 moveto
+66.19 61.07 lineto
+76.53 63.39 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+236 47.4 moveto 48 (RR: [2]) alignedtext
+grestore
+% AGA->AAA
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 441.7 68.9 moveto
+421.47 71.27 395.99 76.5 376 88 curveto
+372.5 90.02 369.11 92.39 365.88 95 curveto
+stroke
+0 0 0 edgecolor
+newpath 363.3 92.61 moveto
+358.17 101.88 lineto
+367.96 97.83 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 363.3 92.61 moveto
+358.17 101.88 lineto
+367.96 97.83 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+377.5 93.4 moveto 45 (FF: [2]) alignedtext
+grestore
+% AAA->AAC
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 301.89 124.63 moveto
+296.11 122.3 289.97 120.24 284 119 curveto
+263.11 114.66 256.97 115.11 236 119 curveto
+233.15 119.53 230.25 120.21 227.35 121 curveto
+stroke
+0 1 1 edgecolor
+newpath 226.11 117.72 moveto
+217.6 124.03 lineto
+228.19 124.4 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 226.11 117.72 moveto
+217.6 124.03 lineto
+228.19 124.4 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+236 124.4 moveto 48 (RR: [1]) alignedtext
+grestore
+% AAA->AGA
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 358.29 133.33 moveto
+377.57 128.75 403.26 121.2 424 110 curveto
+427.23 108.26 430.45 106.29 433.61 104.19 curveto
+stroke
+0 1 1 edgecolor
+newpath 435.69 107.01 moveto
+441.82 98.37 lineto
+431.64 101.3 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 435.69 107.01 moveto
+441.82 98.37 lineto
+431.64 101.3 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+376 133.4 moveto 48 (RR: [2]) alignedtext
+grestore
+endpage
+showpage
+grestore
+%%PageTrailer
+%%EndPage: 1
+%%Trailer
+%%Pages: 1
+%%BoundingBox: 36 36 554 248
+end
+restore
+%%EOF
diff --git a/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/txt b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/txt
new file mode 100755
index 0000000..509d537
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/BubbleMerge/SimpleBubble/txt
@@ -0,0 +1,4 @@
+TAA {[{AAC:[1]}, {AGA:[2]}] [] [] [] {5':[(2-0_0),(1-0_0)], ~5':[]}TAA 2.0x}
+AAA {[] [] [] [{AGA:[2]}, {AAC:[1]}] {5':[], ~5':[]}AAA 2.0x}
+AGA {[{AAA:[2]}] [] [] [{TAA:[2]}] {5':[], ~5':[]}AAGAA 1.0x}
+AAC {[{AAA:[1]}] [] [] [{TAA:[1]}] {5':[], ~5':[]}AACAA 1.0x}
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/FRandRF/..binmerge.crc b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/FRandRF/..binmerge.crc
new file mode 100644
index 0000000..664458d
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/FRandRF/..binmerge.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/FRandRF/.binmerge b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/FRandRF/.binmerge
new file mode 100755
index 0000000..a43b7a0
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/FRandRF/.binmerge
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/FRandRF/bin/.part-00000.crc b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/FRandRF/bin/.part-00000.crc
new file mode 100644
index 0000000..93c484f
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/FRandRF/bin/.part-00000.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/FRandRF/bin/part-00000 b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/FRandRF/bin/part-00000
new file mode 100755
index 0000000..ae4819a
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/FRandRF/bin/part-00000
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/FRandRF/data b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/FRandRF/data
new file mode 100644
index 0000000..115b556
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/FRandRF/data
@@ -0,0 +1,10 @@
+TCA {[{CAG:[2]}] [] [] [{CTC:[2]}] {5':[], ~5':[]} 1.0x}
+AGA {[] [{ATC:[2]}] [] [{CAG:[2]}] {5':[], ~5':[]} 1.0x}
+CGA {[] [{ATC:[1]}] [] [{ACG:[1]}] {5':[], ~5':[]} 1.0x}
+CTA {[] [{GTA:[1]}] [{AGG:[1]}] [] {5':[], ~5':[]} 1.0x}
+GTA {[] [{CTA:[1]}] [{ACG:[1]}] [] {5':[], ~5':[]} 1.0x}
+ATC {[] [{CGA:[1]}, {AGA:[2]}] [] [] {5':[], ~5':[]} 2.0x}
+CTC {[{TCA:[2]}] [] [{AGG:[2]}] [] {5':[], ~5':[]} 1.0x}
+CAG {[{AGA:[2]}] [] [] [{TCA:[2]}] {5':[], ~5':[]} 1.0x}
+ACG {[{CGA:[1]}] [] [{GTA:[1]}] [] {5':[], ~5':[]} 1.0x}
+AGG {[] [] [{CTA:[1]}, {CTC:[2]}] [] {5':[], ~5':[(2-0_0),(1-0_0)]} 2.0x}
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/FRandRF/graphviz/result.ps b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/FRandRF/graphviz/result.ps
new file mode 100644
index 0000000..662de8c
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/FRandRF/graphviz/result.ps
@@ -0,0 +1,1058 @@
+%!PS-Adobe-3.0
+%%Creator: graphviz version 2.26.3 (20100126.1600)
+%%Title: G
+%%Pages: (atend)
+%%BoundingBox: (atend)
+%%EndComments
+save
+%%BeginProlog
+/DotDict 200 dict def
+DotDict begin
+
+/setupLatin1 {
+mark
+/EncodingVector 256 array def
+ EncodingVector 0
+
+ISOLatin1Encoding 0 255 getinterval putinterval
+EncodingVector 45 /hyphen put
+
+% Set up ISO Latin 1 character encoding
+/starnetISO {
+ dup dup findfont dup length dict begin
+ { 1 index /FID ne { def }{ pop pop } ifelse
+ } forall
+ /Encoding EncodingVector def
+ currentdict end definefont
+} def
+/Times-Roman starnetISO def
+/Times-Italic starnetISO def
+/Times-Bold starnetISO def
+/Times-BoldItalic starnetISO def
+/Helvetica starnetISO def
+/Helvetica-Oblique starnetISO def
+/Helvetica-Bold starnetISO def
+/Helvetica-BoldOblique starnetISO def
+/Courier starnetISO def
+/Courier-Oblique starnetISO def
+/Courier-Bold starnetISO def
+/Courier-BoldOblique starnetISO def
+cleartomark
+} bind def
+
+%%BeginResource: procset graphviz 0 0
+/coord-font-family /Times-Roman def
+/default-font-family /Times-Roman def
+/coordfont coord-font-family findfont 8 scalefont def
+
+/InvScaleFactor 1.0 def
+/set_scale {
+ dup 1 exch div /InvScaleFactor exch def
+ scale
+} bind def
+
+% styles
+/solid { [] 0 setdash } bind def
+/dashed { [9 InvScaleFactor mul dup ] 0 setdash } bind def
+/dotted { [1 InvScaleFactor mul 6 InvScaleFactor mul] 0 setdash } bind def
+/invis {/fill {newpath} def /stroke {newpath} def /show {pop newpath} def} bind def
+/bold { 2 setlinewidth } bind def
+/filled { } bind def
+/unfilled { } bind def
+/rounded { } bind def
+/diagonals { } bind def
+
+% hooks for setting color
+/nodecolor { sethsbcolor } bind def
+/edgecolor { sethsbcolor } bind def
+/graphcolor { sethsbcolor } bind def
+/nopcolor {pop pop pop} bind def
+
+/beginpage { % i j npages
+ /npages exch def
+ /j exch def
+ /i exch def
+ /str 10 string def
+ npages 1 gt {
+ gsave
+ coordfont setfont
+ 0 0 moveto
+ (\() show i str cvs show (,) show j str cvs show (\)) show
+ grestore
+ } if
+} bind def
+
+/set_font {
+ findfont exch
+ scalefont setfont
+} def
+
+% draw text fitted to its expected width
+/alignedtext { % width text
+ /text exch def
+ /width exch def
+ gsave
+ width 0 gt {
+ [] 0 setdash
+ text stringwidth pop width exch sub text length div 0 text ashow
+ } if
+ grestore
+} def
+
+/boxprim { % xcorner ycorner xsize ysize
+ 4 2 roll
+ moveto
+ 2 copy
+ exch 0 rlineto
+ 0 exch rlineto
+ pop neg 0 rlineto
+ closepath
+} bind def
+
+/ellipse_path {
+ /ry exch def
+ /rx exch def
+ /y exch def
+ /x exch def
+ matrix currentmatrix
+ newpath
+ x y translate
+ rx ry scale
+ 0 0 1 0 360 arc
+ setmatrix
+} bind def
+
+/endpage { showpage } bind def
+/showpage { } def
+
+/layercolorseq
+ [ % layer color sequence - darkest to lightest
+ [0 0 0]
+ [.2 .8 .8]
+ [.4 .8 .8]
+ [.6 .8 .8]
+ [.8 .8 .8]
+ ]
+def
+
+/layerlen layercolorseq length def
+
+/setlayer {/maxlayer exch def /curlayer exch def
+ layercolorseq curlayer 1 sub layerlen mod get
+ aload pop sethsbcolor
+ /nodecolor {nopcolor} def
+ /edgecolor {nopcolor} def
+ /graphcolor {nopcolor} def
+} bind def
+
+/onlayer { curlayer ne {invis} if } def
+
+/onlayers {
+ /myupper exch def
+ /mylower exch def
+ curlayer mylower lt
+ curlayer myupper gt
+ or
+ {invis} if
+} def
+
+/curlayer 0 def
+
+%%EndResource
+%%EndProlog
+%%BeginSetup
+14 default-font-family set_font
+1 setmiterlimit
+% /arrowlength 10 def
+% /arrowwidth 5 def
+
+% make sure pdfmark is harmless for PS-interpreters other than Distiller
+/pdfmark where {pop} {userdict /pdfmark /cleartomark load put} ifelse
+% make '<<' and '>>' safe on PS Level 1 devices
+/languagelevel where {pop languagelevel}{1} ifelse
+2 lt {
+ userdict (<<) cvn ([) cvn load put
+ userdict (>>) cvn ([) cvn load put
+} if
+
+%%EndSetup
+setupLatin1
+%%Page: 1 1
+%%PageBoundingBox: 36 36 1370 235
+%%PageOrientation: Portrait
+0 0 1 beginpage
+gsave
+36 36 1334 199 boxprim clip newpath
+1 1 set_scale 0 rotate 40 41 translate
+% TCA
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 6 moveto
+0 110 lineto
+56 110 lineto
+56 6 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+14 93.4 moveto 28 (TCA) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 84 moveto
+56 84 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+14 67.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 58 moveto
+56 58 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+8 41.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 0 32 moveto
+56 32 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+16.5 15.4 moveto 23 (1.0) alignedtext
+grestore
+% CAG
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 140 69 moveto
+140 173 lineto
+196 173 lineto
+196 69 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+152.5 156.4 moveto 31 (CAG) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 140 147 moveto
+196 147 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+154 130.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 140 121 moveto
+196 121 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+148 104.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 140 95 moveto
+196 95 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+156.5 78.4 moveto 23 (1.0) alignedtext
+grestore
+% TCA->CAG
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 56 85.12 moveto
+61.65 89.58 67.77 93.78 74 97 curveto
+91.26 105.91 112.06 111.67 129.69 115.3 curveto
+stroke
+0 0 0 edgecolor
+newpath 129.18 118.76 moveto
+139.66 117.2 lineto
+130.49 111.89 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 129.18 118.76 moveto
+139.66 117.2 lineto
+130.49 111.89 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+75.5 118.4 moveto 45 (FF: [2]) alignedtext
+grestore
+% CTC
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1270 7 moveto
+1270 111 lineto
+1326 111 lineto
+1326 7 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1284 94.4 moveto 28 (CTC) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1270 85 moveto
+1326 85 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1284 68.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1270 59 moveto
+1326 59 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1278 42.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1270 33 moveto
+1326 33 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1286.5 16.4 moveto 23 (1.0) alignedtext
+grestore
+% TCA->CTC
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 56.03 52.57 moveto
+84.21 47.6 128.95 41 168 41 curveto
+168 41 168 41 1149 41 curveto
+1186.88 41 1229.78 46.8 1259.79 51.82 curveto
+stroke
+0 1 1 edgecolor
+newpath 1259.39 55.3 moveto
+1269.84 53.55 lineto
+1260.57 48.4 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 1259.39 55.3 moveto
+1269.84 53.55 lineto
+1260.57 48.4 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+630 46.4 moveto 48 (RR: [2]) alignedtext
+grestore
+% CAG->TCA
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 139.99 87.84 moveto
+134.48 82.9 128.4 78.35 122 75 curveto
+104.93 66.06 83.99 61.74 66.21 59.68 curveto
+stroke
+0 1 1 edgecolor
+newpath 66.45 56.18 moveto
+56.16 58.71 lineto
+65.78 63.15 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 66.45 56.18 moveto
+56.16 58.71 lineto
+65.78 63.15 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+74 80.4 moveto 48 (RR: [2]) alignedtext
+grestore
+% AGA
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 280 69 moveto
+280 173 lineto
+336 173 lineto
+336 69 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+292.5 156.4 moveto 31 (AGA) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 280 147 moveto
+336 147 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+294 130.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 280 121 moveto
+336 121 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+288 104.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 280 95 moveto
+336 95 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+296.5 78.4 moveto 23 (1.0) alignedtext
+grestore
+% CAG->AGA
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 196.33 121 moveto
+217.39 121 246.37 121 269.53 121 curveto
+stroke
+0 0 0 edgecolor
+newpath 269.71 124.5 moveto
+279.71 121 lineto
+269.71 117.5 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 269.71 124.5 moveto
+279.71 121 lineto
+269.71 117.5 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+215.5 126.4 moveto 45 (FF: [2]) alignedtext
+grestore
+% CTC->TCA
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 1269.91 40.49 moveto
+1240.88 23.19 1193.65 0 1149 0 curveto
+168 0 168 0 168 0 curveto
+130.89 0 92.17 17.61 64.88 33.42 curveto
+stroke
+0 0 0 edgecolor
+newpath 62.87 30.55 moveto
+56.09 38.69 lineto
+66.46 36.55 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 62.87 30.55 moveto
+56.09 38.69 lineto
+66.46 36.55 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+631.5 5.4 moveto 45 (FF: [2]) alignedtext
+grestore
+% AGG
+gsave
+0 0 0.75294 nodecolor
+newpath 1110 69 moveto
+1110 173 lineto
+1188 173 lineto
+1188 69 lineto
+closepath fill
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 1110 69 moveto
+1110 173 lineto
+1188 173 lineto
+1188 69 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1132.5 156.4 moveto 33 (AGG) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 1110 147 moveto
+1188 147 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1135 130.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 1110 121 moveto
+1188 121 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1118 104.4 moveto 62 (~5':[2,1]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 1110 95 moveto
+1188 95 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1137.5 78.4 moveto 23 (2.0) alignedtext
+grestore
+% CTC->AGG
+gsave
+1 setlinewidth
+0.33333 1 1 edgecolor
+newpath 1269.66 62.03 moveto
+1250.96 64.77 1226.26 69.84 1206 79 curveto
+1202.98 80.37 1199.96 81.91 1196.97 83.58 curveto
+stroke
+0.33333 1 1 edgecolor
+newpath 1194.9 80.75 moveto
+1188.16 88.92 lineto
+1198.53 86.73 lineto
+closepath fill
+1 setlinewidth
+solid
+0.33333 1 1 edgecolor
+newpath 1194.9 80.75 moveto
+1188.16 88.92 lineto
+1198.53 86.73 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+1206 84.4 moveto 46 (RF: [2]) alignedtext
+grestore
+% AGA->CAG
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 279.89 106.63 moveto
+274.11 104.3 267.97 102.24 262 101 curveto
+241.11 96.66 234.89 96.66 214 101 curveto
+211.2 101.58 208.37 102.34 205.55 103.23 curveto
+stroke
+0 1 1 edgecolor
+newpath 204.33 99.95 moveto
+196.11 106.63 lineto
+206.71 106.53 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 204.33 99.95 moveto
+196.11 106.63 lineto
+206.71 106.53 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+214 106.4 moveto 48 (RR: [2]) alignedtext
+grestore
+% ATC
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 418 80 moveto
+418 184 lineto
+474 184 lineto
+474 80 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+432 167.4 moveto 28 (ATC) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 418 158 moveto
+474 158 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+432 141.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 418 132 moveto
+474 132 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+426 115.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 418 106 moveto
+474 106 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+434.5 89.4 moveto 23 (2.0) alignedtext
+grestore
+% AGA->ATC
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 336.1 127.29 moveto
+341.99 128.38 348.17 129.37 354 130 curveto
+371.46 131.88 390.89 132.52 407.37 132.63 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 407.73 136.13 moveto
+417.73 132.63 lineto
+407.74 129.13 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 407.73 136.13 moveto
+417.73 132.63 lineto
+407.74 129.13 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+354 137.4 moveto 46 (FR: [2]) alignedtext
+grestore
+% ATC->AGA
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 417.64 114.54 moveto
+411.98 111.84 405.95 109.46 400 108 curveto
+382.48 103.71 362.72 105.64 346.02 109.18 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 344.97 105.84 moveto
+336.06 111.56 lineto
+346.59 112.64 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 344.97 105.84 moveto
+336.06 111.56 lineto
+346.59 112.64 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+354 113.4 moveto 46 (FR: [2]) alignedtext
+grestore
+% CGA
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 556 70 moveto
+556 174 lineto
+612 174 lineto
+612 70 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+568.5 157.4 moveto 31 (CGA) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 556 148 moveto
+612 148 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+570 131.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 556 122 moveto
+612 122 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+564 105.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 556 96 moveto
+612 96 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+572.5 79.4 moveto 23 (1.0) alignedtext
+grestore
+% ATC->CGA
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 474.26 129.95 moveto
+494.82 128.46 522.89 126.43 545.5 124.79 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 546.06 128.26 moveto
+555.78 124.05 lineto
+545.55 121.28 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 546.06 128.26 moveto
+555.78 124.05 lineto
+545.55 121.28 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+492 133.4 moveto 46 (FR: [1]) alignedtext
+grestore
+% CGA->ATC
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 555.82 100.07 moveto
+550.19 96.74 544.12 93.82 538 92 curveto
+518.4 86.17 511.15 84.84 492 92 curveto
+488.73 93.22 485.54 94.8 482.46 96.61 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 480.43 93.75 moveto
+474.11 102.25 lineto
+484.35 99.55 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 480.43 93.75 moveto
+474.11 102.25 lineto
+484.35 99.55 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+492 97.4 moveto 46 (FR: [1]) alignedtext
+grestore
+% ACG
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 696 87 moveto
+696 191 lineto
+752 191 lineto
+752 87 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+708.5 174.4 moveto 31 (ACG) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 696 165 moveto
+752 165 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+710 148.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 696 139 moveto
+752 139 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+704 122.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 696 113 moveto
+752 113 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+712.5 96.4 moveto 23 (1.0) alignedtext
+grestore
+% CGA->ACG
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 612.33 125.44 moveto
+633.39 128 662.37 131.52 685.53 134.33 curveto
+stroke
+0 1 1 edgecolor
+newpath 685.36 137.83 moveto
+695.71 135.56 lineto
+686.21 130.88 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 685.36 137.83 moveto
+695.71 135.56 lineto
+686.21 130.88 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+630 138.4 moveto 48 (RR: [1]) alignedtext
+grestore
+% ACG->CGA
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 695.88 114 moveto
+690.3 110.3 684.23 107.05 678 105 curveto
+659.96 99.06 639.25 101.83 621.87 106.72 curveto
+stroke
+0 0 0 edgecolor
+newpath 620.56 103.46 moveto
+612.06 109.79 lineto
+622.65 110.14 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 620.56 103.46 moveto
+612.06 109.79 lineto
+622.65 110.14 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+631.5 110.4 moveto 45 (FF: [1]) alignedtext
+grestore
+% GTA
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 834 77 moveto
+834 181 lineto
+890 181 lineto
+890 77 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+847.5 164.4 moveto 29 (GTA) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 834 155 moveto
+890 155 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+848 138.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 834 129 moveto
+890 129 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+842 112.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 834 103 moveto
+890 103 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+850.5 86.4 moveto 23 (1.0) alignedtext
+grestore
+% ACG->GTA
+gsave
+1 setlinewidth
+0.33333 1 1 edgecolor
+newpath 752.26 136.95 moveto
+772.82 135.46 800.89 133.43 823.5 131.79 curveto
+stroke
+0.33333 1 1 edgecolor
+newpath 824.06 135.26 moveto
+833.78 131.05 lineto
+823.55 128.28 lineto
+closepath fill
+1 setlinewidth
+solid
+0.33333 1 1 edgecolor
+newpath 824.06 135.26 moveto
+833.78 131.05 lineto
+823.55 128.28 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+770 140.4 moveto 46 (RF: [1]) alignedtext
+grestore
+% CTA
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 972 72 moveto
+972 176 lineto
+1028 176 lineto
+1028 72 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+986 159.4 moveto 28 (CTA) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 972 150 moveto
+1028 150 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+986 133.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 972 124 moveto
+1028 124 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+980 107.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 972 98 moveto
+1028 98 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+988.5 81.4 moveto 23 (1.0) alignedtext
+grestore
+% CTA->GTA
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 971.97 98.28 moveto
+966.37 94.47 960.28 91.12 954 89 curveto
+934.63 82.47 927.15 81.84 908 89 curveto
+904.73 90.22 901.54 91.8 898.46 93.61 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 896.43 90.75 moveto
+890.11 99.25 lineto
+900.35 96.55 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 896.43 90.75 moveto
+890.11 99.25 lineto
+900.35 96.55 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+908 94.4 moveto 46 (FR: [1]) alignedtext
+grestore
+% CTA->AGG
+gsave
+1 setlinewidth
+0.33333 1 1 edgecolor
+newpath 1028.03 123.44 moveto
+1048.15 123.03 1075.8 122.47 1099.59 121.99 curveto
+stroke
+0.33333 1 1 edgecolor
+newpath 1099.93 125.49 moveto
+1109.86 121.79 lineto
+1099.79 118.49 lineto
+closepath fill
+1 setlinewidth
+solid
+0.33333 1 1 edgecolor
+newpath 1099.93 125.49 moveto
+1109.86 121.79 lineto
+1099.79 118.49 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+1046 128.4 moveto 46 (RF: [1]) alignedtext
+grestore
+% GTA->ACG
+gsave
+1 setlinewidth
+0.33333 1 1 edgecolor
+newpath 833.82 107.07 moveto
+828.19 103.74 822.12 100.82 816 99 curveto
+796.4 93.17 789.15 91.84 770 99 curveto
+766.73 100.22 763.54 101.8 760.46 103.61 curveto
+stroke
+0.33333 1 1 edgecolor
+newpath 758.43 100.75 moveto
+752.11 109.25 lineto
+762.35 106.55 lineto
+closepath fill
+1 setlinewidth
+solid
+0.33333 1 1 edgecolor
+newpath 758.43 100.75 moveto
+752.11 109.25 lineto
+762.35 106.55 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+770 104.4 moveto 46 (RF: [1]) alignedtext
+grestore
+% GTA->CTA
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 890.26 127.98 moveto
+910.82 127.23 938.89 126.21 961.5 125.39 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 961.91 128.88 moveto
+971.78 125.02 lineto
+961.66 121.89 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 961.91 128.88 moveto
+971.78 125.02 lineto
+961.66 121.89 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+908 132.4 moveto 46 (FR: [1]) alignedtext
+grestore
+% AGG->CTC
+gsave
+1 setlinewidth
+0.33333 1 1 edgecolor
+newpath 1188.11 116.24 moveto
+1207.99 112.76 1232.09 106.86 1252 97 curveto
+1255.3 95.36 1258.58 93.45 1261.77 91.36 curveto
+stroke
+0.33333 1 1 edgecolor
+newpath 1263.86 94.17 moveto
+1269.97 85.52 lineto
+1259.8 88.47 lineto
+closepath fill
+1 setlinewidth
+solid
+0.33333 1 1 edgecolor
+newpath 1263.86 94.17 moveto
+1269.97 85.52 lineto
+1259.8 88.47 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+1206 117.4 moveto 46 (RF: [2]) alignedtext
+grestore
+% AGG->CTA
+gsave
+1 setlinewidth
+0.33333 1 1 edgecolor
+newpath 1109.95 104.57 moveto
+1104.03 102.68 1097.92 101.06 1092 100 curveto
+1071.87 96.41 1065.86 95.13 1046 100 curveto
+1043.21 100.68 1040.4 101.57 1037.63 102.6 curveto
+stroke
+0.33333 1 1 edgecolor
+newpath 1036.19 99.4 moveto
+1028.36 106.54 lineto
+1038.93 105.84 lineto
+closepath fill
+1 setlinewidth
+solid
+0.33333 1 1 edgecolor
+newpath 1036.19 99.4 moveto
+1028.36 106.54 lineto
+1038.93 105.84 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+1046 105.4 moveto 46 (RF: [1]) alignedtext
+grestore
+endpage
+showpage
+grestore
+%%PageTrailer
+%%EndPage: 1
+%%Trailer
+%%Pages: 1
+%%BoundingBox: 36 36 1370 235
+end
+restore
+%%EOF
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/InvalidBubble/..binmerge.crc b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/InvalidBubble/..binmerge.crc
deleted file mode 100644
index 9fd1d09..0000000
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/InvalidBubble/..binmerge.crc
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/InvalidBubble/.binmerge b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/InvalidBubble/.binmerge
deleted file mode 100755
index 23ce1ef..0000000
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/InvalidBubble/.binmerge
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/InvalidBubble/bin/.part-00000.crc b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/InvalidBubble/bin/.part-00000.crc
deleted file mode 100644
index 3336d8b..0000000
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/InvalidBubble/bin/.part-00000.crc
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/InvalidBubble/bin/part-00000 b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/InvalidBubble/bin/part-00000
deleted file mode 100755
index dc166fb..0000000
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/InvalidBubble/bin/part-00000
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/InvalidBubble/data b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/InvalidBubble/data
deleted file mode 100644
index a75b2c5..0000000
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/InvalidBubble/data
+++ /dev/null
@@ -1,8 +0,0 @@
-AAA {[] [] [] [{GAA:[3]}, {CAA:[6]}] {5':[], ~5':[(3-0_0)]} 2.0x}
-CAA {[{AAA:[6]}] [] [] [{ACA:[5]}] {5':[(6-0_0)], ~5':[(5-0_0)]} 2.0x}
-GAA {[{AAA:[3]}] [] [] [{AGA:[2]}] {5':[], ~5':[]} 2.0x}
-TAA {[{AAG:[1]}, {AAC:[4]}] [] [] [] {5':[(4-0_0)], ~5':[]} 2.0x}
-ACA {[{CAA:[5]}] [] [] [{AAC:[5]}] {5':[], ~5':[]} 1.0x}
-AGA {[{GAA:[2]}] [] [] [{AAG:[2]}] {5':[], ~5':[]} 1.0x}
-AAC {[{ACA:[5]}] [] [] [{TAA:[4]}] {5':[], ~5':[]} 2.0x}
-AAG {[{AGA:[2]}] [] [] [{TAA:[1]}] {5':[(2-0_0)], ~5':[(1-0_0)]} 2.0x}
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/InvalidBubble/graphviz/result.ps b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/InvalidBubble/graphviz/result.ps
deleted file mode 100644
index 43e912f..0000000
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/InvalidBubble/graphviz/result.ps
+++ /dev/null
@@ -1,918 +0,0 @@
-%!PS-Adobe-3.0
-%%Creator: graphviz version 2.26.3 (20100126.1600)
-%%Title: G
-%%Pages: (atend)
-%%BoundingBox: (atend)
-%%EndComments
-save
-%%BeginProlog
-/DotDict 200 dict def
-DotDict begin
-
-/setupLatin1 {
-mark
-/EncodingVector 256 array def
- EncodingVector 0
-
-ISOLatin1Encoding 0 255 getinterval putinterval
-EncodingVector 45 /hyphen put
-
-% Set up ISO Latin 1 character encoding
-/starnetISO {
- dup dup findfont dup length dict begin
- { 1 index /FID ne { def }{ pop pop } ifelse
- } forall
- /Encoding EncodingVector def
- currentdict end definefont
-} def
-/Times-Roman starnetISO def
-/Times-Italic starnetISO def
-/Times-Bold starnetISO def
-/Times-BoldItalic starnetISO def
-/Helvetica starnetISO def
-/Helvetica-Oblique starnetISO def
-/Helvetica-Bold starnetISO def
-/Helvetica-BoldOblique starnetISO def
-/Courier starnetISO def
-/Courier-Oblique starnetISO def
-/Courier-Bold starnetISO def
-/Courier-BoldOblique starnetISO def
-cleartomark
-} bind def
-
-%%BeginResource: procset graphviz 0 0
-/coord-font-family /Times-Roman def
-/default-font-family /Times-Roman def
-/coordfont coord-font-family findfont 8 scalefont def
-
-/InvScaleFactor 1.0 def
-/set_scale {
- dup 1 exch div /InvScaleFactor exch def
- scale
-} bind def
-
-% styles
-/solid { [] 0 setdash } bind def
-/dashed { [9 InvScaleFactor mul dup ] 0 setdash } bind def
-/dotted { [1 InvScaleFactor mul 6 InvScaleFactor mul] 0 setdash } bind def
-/invis {/fill {newpath} def /stroke {newpath} def /show {pop newpath} def} bind def
-/bold { 2 setlinewidth } bind def
-/filled { } bind def
-/unfilled { } bind def
-/rounded { } bind def
-/diagonals { } bind def
-
-% hooks for setting color
-/nodecolor { sethsbcolor } bind def
-/edgecolor { sethsbcolor } bind def
-/graphcolor { sethsbcolor } bind def
-/nopcolor {pop pop pop} bind def
-
-/beginpage { % i j npages
- /npages exch def
- /j exch def
- /i exch def
- /str 10 string def
- npages 1 gt {
- gsave
- coordfont setfont
- 0 0 moveto
- (\() show i str cvs show (,) show j str cvs show (\)) show
- grestore
- } if
-} bind def
-
-/set_font {
- findfont exch
- scalefont setfont
-} def
-
-% draw text fitted to its expected width
-/alignedtext { % width text
- /text exch def
- /width exch def
- gsave
- width 0 gt {
- [] 0 setdash
- text stringwidth pop width exch sub text length div 0 text ashow
- } if
- grestore
-} def
-
-/boxprim { % xcorner ycorner xsize ysize
- 4 2 roll
- moveto
- 2 copy
- exch 0 rlineto
- 0 exch rlineto
- pop neg 0 rlineto
- closepath
-} bind def
-
-/ellipse_path {
- /ry exch def
- /rx exch def
- /y exch def
- /x exch def
- matrix currentmatrix
- newpath
- x y translate
- rx ry scale
- 0 0 1 0 360 arc
- setmatrix
-} bind def
-
-/endpage { showpage } bind def
-/showpage { } def
-
-/layercolorseq
- [ % layer color sequence - darkest to lightest
- [0 0 0]
- [.2 .8 .8]
- [.4 .8 .8]
- [.6 .8 .8]
- [.8 .8 .8]
- ]
-def
-
-/layerlen layercolorseq length def
-
-/setlayer {/maxlayer exch def /curlayer exch def
- layercolorseq curlayer 1 sub layerlen mod get
- aload pop sethsbcolor
- /nodecolor {nopcolor} def
- /edgecolor {nopcolor} def
- /graphcolor {nopcolor} def
-} bind def
-
-/onlayer { curlayer ne {invis} if } def
-
-/onlayers {
- /myupper exch def
- /mylower exch def
- curlayer mylower lt
- curlayer myupper gt
- or
- {invis} if
-} def
-
-/curlayer 0 def
-
-%%EndResource
-%%EndProlog
-%%BeginSetup
-14 default-font-family set_font
-1 setmiterlimit
-% /arrowlength 10 def
-% /arrowwidth 5 def
-
-% make sure pdfmark is harmless for PS-interpreters other than Distiller
-/pdfmark where {pop} {userdict /pdfmark /cleartomark load put} ifelse
-% make '<<' and '>>' safe on PS Level 1 devices
-/languagelevel where {pop languagelevel}{1} ifelse
-2 lt {
- userdict (<<) cvn ([) cvn load put
- userdict (>>) cvn ([) cvn load put
-} if
-
-%%EndSetup
-setupLatin1
-%%Page: 1 1
-%%PageBoundingBox: 36 36 1110 232
-%%PageOrientation: Portrait
-0 0 1 beginpage
-gsave
-36 36 1074 196 boxprim clip newpath
-1 1 set_scale 0 rotate 40 41 translate
-% AAA
-gsave
-0 0 0.75294 nodecolor
-newpath .5 6 moveto
-.5 110 lineto
-65.5 110 lineto
-65.5 6 lineto
-closepath fill
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath .5 6 moveto
-.5 110 lineto
-65.5 110 lineto
-65.5 6 lineto
-closepath stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-17.5 93.4 moveto 31 (AAA) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath .5 84 moveto
-65.5 84 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-19 67.4 moveto 28 (5':[]) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath .5 58 moveto
-65.5 58 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-8.5 41.4 moveto 49 (~5':[3]) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath .5 32 moveto
-65.5 32 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-21.5 15.4 moveto 23 (2.0) alignedtext
-grestore
-% GAA
-gsave
-1 setlinewidth
-0 0 0 nodecolor
-newpath 150 69 moveto
-150 173 lineto
-206 173 lineto
-206 69 lineto
-closepath stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-162 156.4 moveto 32 (GAA) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 150 147 moveto
-206 147 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-164 130.4 moveto 28 (5':[]) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 150 121 moveto
-206 121 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-158 104.4 moveto 40 (~5':[]) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 150 95 moveto
-206 95 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-166.5 78.4 moveto 23 (2.0) alignedtext
-grestore
-% AAA->GAA
-gsave
-1 setlinewidth
-0 1 1 edgecolor
-newpath 65.76 86.05 moveto
-71.58 90.14 77.78 93.99 84 97 curveto
-101.48 105.48 122.3 111.19 139.89 114.9 curveto
-stroke
-0 1 1 edgecolor
-newpath 139.34 118.36 moveto
-149.83 116.87 lineto
-140.7 111.49 lineto
-closepath fill
-1 setlinewidth
-solid
-0 1 1 edgecolor
-newpath 139.34 118.36 moveto
-149.83 116.87 lineto
-140.7 111.49 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-84 118.4 moveto 48 (RR: [3]) alignedtext
-grestore
-% CAA
-gsave
-0 0 0.75294 nodecolor
-newpath 1000.5 7 moveto
-1000.5 111 lineto
-1065.5 111 lineto
-1065.5 7 lineto
-closepath fill
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 1000.5 7 moveto
-1000.5 111 lineto
-1065.5 111 lineto
-1065.5 7 lineto
-closepath stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-1017.5 94.4 moveto 31 (CAA) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 1000.5 85 moveto
-1065.5 85 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-1014.5 68.4 moveto 37 (5':[6]) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 1000.5 59 moveto
-1065.5 59 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-1008.5 42.4 moveto 49 (~5':[5]) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 1000.5 33 moveto
-1065.5 33 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-1021.5 16.4 moveto 23 (2.0) alignedtext
-grestore
-% AAA->CAA
-gsave
-1 setlinewidth
-0 1 1 edgecolor
-newpath 65.7 51.96 moveto
-95 47.07 139.22 41 178 41 curveto
-178 41 178 41 888 41 curveto
-922.57 41 961.42 46.1 990.2 50.87 curveto
-stroke
-0 1 1 edgecolor
-newpath 989.87 54.37 moveto
-1000.32 52.6 lineto
-991.05 47.47 lineto
-closepath fill
-1 setlinewidth
-solid
-0 1 1 edgecolor
-newpath 989.87 54.37 moveto
-1000.32 52.6 lineto
-991.05 47.47 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-514 46.4 moveto 48 (RR: [6]) alignedtext
-grestore
-% GAA->AAA
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 149.76 87.56 moveto
-144.31 82.72 138.32 78.27 132 75 curveto
-114.83 66.11 93.97 61.73 75.83 59.63 curveto
-stroke
-0 0 0 edgecolor
-newpath 76.08 56.13 moveto
-65.79 58.65 lineto
-75.41 63.1 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 76.08 56.13 moveto
-65.79 58.65 lineto
-75.41 63.1 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-85.5 80.4 moveto 45 (FF: [3]) alignedtext
-grestore
-% AGA
-gsave
-1 setlinewidth
-0 0 0 nodecolor
-newpath 290 80 moveto
-290 184 lineto
-346 184 lineto
-346 80 lineto
-closepath stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-302.5 167.4 moveto 31 (AGA) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 290 158 moveto
-346 158 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-304 141.4 moveto 28 (5':[]) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 290 132 moveto
-346 132 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-298 115.4 moveto 40 (~5':[]) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 290 106 moveto
-346 106 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-306.5 89.4 moveto 23 (1.0) alignedtext
-grestore
-% GAA->AGA
-gsave
-1 setlinewidth
-0 1 1 edgecolor
-newpath 206.1 127.29 moveto
-211.99 128.39 218.17 129.37 224 130 curveto
-242.28 131.97 262.67 132.59 279.77 132.67 curveto
-stroke
-0 1 1 edgecolor
-newpath 279.95 136.17 moveto
-289.95 132.66 lineto
-279.95 129.17 lineto
-closepath fill
-1 setlinewidth
-solid
-0 1 1 edgecolor
-newpath 279.95 136.17 moveto
-289.95 132.66 lineto
-279.95 129.17 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-224 137.4 moveto 48 (RR: [2]) alignedtext
-grestore
-% CAA->AAA
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 1000.26 37.2 moveto
-971.83 20.39 928.9 0 888 0 curveto
-178 0 178 0 178 0 curveto
-141.06 0 102.36 16.43 74.25 31.8 curveto
-stroke
-0 0 0 edgecolor
-newpath 72.5 28.77 moveto
-65.51 36.73 lineto
-75.94 34.87 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 72.5 28.77 moveto
-65.51 36.73 lineto
-75.94 34.87 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-515.5 5.4 moveto 45 (FF: [6]) alignedtext
-grestore
-% ACA
-gsave
-1 setlinewidth
-0 0 0 nodecolor
-newpath 860 69 moveto
-860 173 lineto
-916 173 lineto
-916 69 lineto
-closepath stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-873 156.4 moveto 30 (ACA) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 860 147 moveto
-916 147 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-874 130.4 moveto 28 (5':[]) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 860 121 moveto
-916 121 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-868 104.4 moveto 40 (~5':[]) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 860 95 moveto
-916 95 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-876.5 78.4 moveto 23 (1.0) alignedtext
-grestore
-% CAA->ACA
-gsave
-1 setlinewidth
-0 1 1 edgecolor
-newpath 1000.35 61.16 moveto
-980.32 63.53 954.64 68.52 934 79 curveto
-930.67 80.69 927.4 82.69 924.24 84.88 curveto
-stroke
-0 1 1 edgecolor
-newpath 921.97 82.21 moveto
-916.14 91.06 lineto
-926.21 87.78 lineto
-closepath fill
-1 setlinewidth
-solid
-0 1 1 edgecolor
-newpath 921.97 82.21 moveto
-916.14 91.06 lineto
-926.21 87.78 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-934 84.4 moveto 48 (RR: [5]) alignedtext
-grestore
-% ACA->CAA
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 916.13 116.78 moveto
-935.35 113.2 961.02 107.01 982 97 curveto
-985.34 95.41 988.67 93.58 991.95 91.61 curveto
-stroke
-0 0 0 edgecolor
-newpath 993.95 94.49 moveto
-1000.45 86.12 lineto
-990.15 88.61 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 993.95 94.49 moveto
-1000.45 86.12 lineto
-990.15 88.61 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-935.5 117.4 moveto 45 (FF: [5]) alignedtext
-grestore
-% AAC
-gsave
-1 setlinewidth
-0 0 0 nodecolor
-newpath 720 74 moveto
-720 178 lineto
-776 178 lineto
-776 74 lineto
-closepath stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-732.5 161.4 moveto 31 (AAC) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 720 152 moveto
-776 152 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-734 135.4 moveto 28 (5':[]) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 720 126 moveto
-776 126 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-728 109.4 moveto 40 (~5':[]) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 720 100 moveto
-776 100 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-736.5 83.4 moveto 23 (2.0) alignedtext
-grestore
-% ACA->AAC
-gsave
-1 setlinewidth
-0 1 1 edgecolor
-newpath 859.97 95.28 moveto
-854.37 91.47 848.28 88.12 842 86 curveto
-821.78 79.18 813.98 78.53 794 86 curveto
-790.73 87.22 787.54 88.8 784.46 90.61 curveto
-stroke
-0 1 1 edgecolor
-newpath 782.43 87.75 moveto
-776.11 96.25 lineto
-786.35 93.55 lineto
-closepath fill
-1 setlinewidth
-solid
-0 1 1 edgecolor
-newpath 782.43 87.75 moveto
-776.11 96.25 lineto
-786.35 93.55 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-794 91.4 moveto 48 (RR: [5]) alignedtext
-grestore
-% AGA->GAA
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 289.64 114.54 moveto
-283.98 111.84 277.95 109.46 272 108 curveto
-253.81 103.54 233.24 105.6 215.99 109.28 curveto
-stroke
-0 0 0 edgecolor
-newpath 215.17 105.87 moveto
-206.25 111.59 lineto
-216.79 112.68 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 215.17 105.87 moveto
-206.25 111.59 lineto
-216.79 112.68 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-225.5 113.4 moveto 45 (FF: [2]) alignedtext
-grestore
-% AAG
-gsave
-0 0 0.75294 nodecolor
-newpath 430.5 70 moveto
-430.5 174 lineto
-495.5 174 lineto
-495.5 70 lineto
-closepath fill
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 430.5 70 moveto
-430.5 174 lineto
-495.5 174 lineto
-495.5 70 lineto
-closepath stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-447 157.4 moveto 32 (AAG) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 430.5 148 moveto
-495.5 148 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-444.5 131.4 moveto 37 (5':[2]) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 430.5 122 moveto
-495.5 122 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-438.5 105.4 moveto 49 (~5':[1]) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 430.5 96 moveto
-495.5 96 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-451.5 79.4 moveto 23 (2.0) alignedtext
-grestore
-% AGA->AAG
-gsave
-1 setlinewidth
-0 1 1 edgecolor
-newpath 346.3 130.05 moveto
-367.34 128.6 396.4 126.59 420.26 124.95 curveto
-stroke
-0 1 1 edgecolor
-newpath 420.73 128.42 moveto
-430.47 124.24 lineto
-420.25 121.44 lineto
-closepath fill
-1 setlinewidth
-solid
-0 1 1 edgecolor
-newpath 420.73 128.42 moveto
-430.47 124.24 lineto
-420.25 121.44 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-364 133.4 moveto 48 (RR: [2]) alignedtext
-grestore
-% TAA
-gsave
-0 0 0.75294 nodecolor
-newpath 580 84 moveto
-580 188 lineto
-636 188 lineto
-636 84 lineto
-closepath fill
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 580 84 moveto
-580 188 lineto
-636 188 lineto
-636 84 lineto
-closepath stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-593.5 171.4 moveto 29 (TAA) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 580 162 moveto
-636 162 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-589.5 145.4 moveto 37 (5':[4]) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 580 136 moveto
-636 136 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-588 119.4 moveto 40 (~5':[]) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 580 110 moveto
-636 110 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-596.5 93.4 moveto 23 (2.0) alignedtext
-grestore
-% TAA->AAG
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 579.88 111 moveto
-574.3 107.3 568.23 104.05 562 102 curveto
-543.73 95.98 522.94 98.79 505.15 103.97 curveto
-stroke
-0 0 0 edgecolor
-newpath 504.05 100.65 moveto
-495.61 107.05 lineto
-506.2 107.31 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 504.05 100.65 moveto
-495.61 107.05 lineto
-506.2 107.31 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-515.5 107.4 moveto 45 (FF: [1]) alignedtext
-grestore
-% TAA->AAC
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 636.33 133.98 moveto
-657.39 132.47 686.37 130.4 709.53 128.75 curveto
-stroke
-0 0 0 edgecolor
-newpath 709.99 132.22 moveto
-719.71 128.02 lineto
-709.49 125.24 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 709.99 132.22 moveto
-719.71 128.02 lineto
-709.49 125.24 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-655.5 137.4 moveto 45 (FF: [4]) alignedtext
-grestore
-% AAG->AGA
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 430.29 107.87 moveto
-424.31 105.85 418.04 104.09 412 103 curveto
-391 99.22 384.5 97.08 364 103 curveto
-361.01 103.86 358.03 104.98 355.11 106.28 curveto
-stroke
-0 0 0 edgecolor
-newpath 353.32 103.27 moveto
-346.01 110.93 lineto
-356.51 109.5 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 353.32 103.27 moveto
-346.01 110.93 lineto
-356.51 109.5 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-365.5 108.4 moveto 45 (FF: [2]) alignedtext
-grestore
-% AAG->TAA
-gsave
-1 setlinewidth
-0 1 1 edgecolor
-newpath 495.54 125.14 moveto
-517.55 127.27 546.71 130.08 569.82 132.31 curveto
-stroke
-0 1 1 edgecolor
-newpath 569.68 135.82 moveto
-579.97 133.29 lineto
-570.35 128.85 lineto
-closepath fill
-1 setlinewidth
-solid
-0 1 1 edgecolor
-newpath 569.68 135.82 moveto
-579.97 133.29 lineto
-570.35 128.85 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-514 136.4 moveto 48 (RR: [1]) alignedtext
-grestore
-% AAC->ACA
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 776.33 124.99 moveto
-797.39 124.24 826.37 123.2 849.53 122.37 curveto
-stroke
-0 0 0 edgecolor
-newpath 849.84 125.87 moveto
-859.71 122.01 lineto
-849.59 118.87 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 849.84 125.87 moveto
-859.71 122.01 lineto
-849.59 118.87 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-795.5 129.4 moveto 45 (FF: [5]) alignedtext
-grestore
-% AAC->TAA
-gsave
-1 setlinewidth
-0 1 1 edgecolor
-newpath 719.83 112.35 moveto
-714.06 110.13 707.93 108.18 702 107 curveto
-681.07 102.85 674.5 101.08 654 107 curveto
-651.01 107.86 648.03 108.98 645.11 110.28 curveto
-stroke
-0 1 1 edgecolor
-newpath 643.32 107.27 moveto
-636.01 114.93 lineto
-646.51 113.5 lineto
-closepath fill
-1 setlinewidth
-solid
-0 1 1 edgecolor
-newpath 643.32 107.27 moveto
-636.01 114.93 lineto
-646.51 113.5 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-654 112.4 moveto 48 (RR: [4]) alignedtext
-grestore
-endpage
-showpage
-grestore
-%%PageTrailer
-%%EndPage: 1
-%%Trailer
-%%Pages: 1
-%%BoundingBox: 36 36 1110 232
-end
-restore
-%%EOF
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoL/..binmerge.crc b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoL/..binmerge.crc
index ceb8449..7b691e0 100644
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoL/..binmerge.crc
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoL/..binmerge.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoL/.binmerge b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoL/.binmerge
index 85ab82c..dfa187d 100755
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoL/.binmerge
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoL/.binmerge
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoL/bin/.part-00000.crc b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoL/bin/.part-00000.crc
index f9c5b61..dc1ffa4 100644
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoL/bin/.part-00000.crc
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoL/bin/.part-00000.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoL/bin/part-00000 b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoL/bin/part-00000
index 50045dd..61c9ac7 100755
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoL/bin/part-00000
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoL/bin/part-00000
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoL/data b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoL/data
index 4acf0c7..58b82de 100644
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoL/data
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoL/data
@@ -1,8 +1,12 @@
-AAA {[] [] [] [{GAA:[6]}, {CAA:[5]}] {5':[], ~5':[]} 2.0x}
-CAA {[{AAA:[5]}] [] [] [{ACA:[3]}] {5':[(5-0_0)], ~5':[]} 2.0x}
-GAA {[{AAA:[6]}] [] [] [{AGA:[4]}] {5':[(6-0_0)], ~5':[(4-0_0)]} 2.0x}
-TAA {[{AAG:[2]}, {AAC:[1]}] [] [] [] {5':[(2-0_0),(1-0_0)], ~5':[]} 2.0x}
-ACA {[{CAA:[3]}] [] [] [{AAC:[3]}] {5':[], ~5':[]} 1.0x}
-AGA {[{GAA:[4]}] [] [] [{AAG:[4]}] {5':[], ~5':[]} 1.0x}
-AAC {[{ACA:[3]}] [] [] [{TAA:[1]}] {5':[(3-0_0)], ~5':[]} 2.0x}
-AAG {[{AGA:[4]}] [] [] [{TAA:[2]}] {5':[], ~5':[]} 2.0x}
+AAA {[{AAG:[1]}] [] [] [{GAA:[1]}] {5':[], ~5':[]} 1.0x}
+GAA {[{AAA:[1]}] [] [] [{CGA:[1]}] {5':[], ~5':[]} 1.0x}
+CCA {[{CAG:[2]}] [] [{GGA:[2]}] [] {5':[], ~5':[]} 1.0x}
+CGA {[{GAA:[1]}] [] [] [{ACG:[1]}] {5':[], ~5':[]} 1.0x}
+GGA {[] [] [{CCA:[2]}] [{AGG:[1]}] {5':[], ~5':[]} 2.0x}
+GCC {[{CCG:[2]}] [] [] [{AGC:[2]}] {5':[], ~5':[]} 1.0x}
+AGC {[{GCC:[2]}] [] [] [{CAG:[2]}] {5':[], ~5':[]} 1.0x}
+AAG {[{AGG:[1]}] [] [] [{AAA:[1]}] {5':[], ~5':[]} 1.0x}
+CAG {[{AGC:[2]}] [] [] [{CCA:[2]}] {5':[], ~5':[]} 1.0x}
+ACG {[{CGA:[1]}] [{CCG:[2]}] [] [] {5':[(2-0_0),(1-0_0)], ~5':[]} 2.0x}
+CCG {[] [{ACG:[2]}] [] [{GCC:[2]}] {5':[], ~5':[]} 1.0x}
+AGG {[{GGA:[1]}] [] [] [{AAG:[1]}] {5':[], ~5':[]} 1.0x}
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoL/graphviz/result.ps b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoL/graphviz/result.ps
index 3abd980..3d02f39 100644
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoL/graphviz/result.ps
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoL/graphviz/result.ps
@@ -178,11 +178,11 @@
%%EndSetup
setupLatin1
%%Page: 1 1
-%%PageBoundingBox: 36 36 1100 232
+%%PageBoundingBox: 36 36 1646 236
%%PageOrientation: Portrait
0 0 1 beginpage
gsave
-36 36 1064 196 boxprim clip newpath
+36 36 1610 200 boxprim clip newpath
1 1 set_scale 0 rotate 40 41 translate
% AAA
gsave
@@ -219,692 +219,1002 @@
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-16.5 15.4 moveto 23 (2.0) alignedtext
-grestore
-% GAA
-gsave
-0 0 0.75294 nodecolor
-newpath 140.5 69 moveto
-140.5 173 lineto
-205.5 173 lineto
-205.5 69 lineto
-closepath fill
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 140.5 69 moveto
-140.5 173 lineto
-205.5 173 lineto
-205.5 69 lineto
-closepath stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-157 156.4 moveto 32 (GAA) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 140.5 147 moveto
-205.5 147 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-154.5 130.4 moveto 37 (5':[6]) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 140.5 121 moveto
-205.5 121 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-148.5 104.4 moveto 49 (~5':[4]) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 140.5 95 moveto
-205.5 95 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-161.5 78.4 moveto 23 (2.0) alignedtext
-grestore
-% AAA->GAA
-gsave
-1 setlinewidth
-0 1 1 edgecolor
-newpath 56.23 85.38 moveto
-61.8 89.76 67.84 93.87 74 97 curveto
-91.48 105.89 112.38 111.58 130.47 115.18 curveto
-stroke
-0 1 1 edgecolor
-newpath 130 118.65 moveto
-140.47 117.01 lineto
-131.26 111.76 lineto
-closepath fill
-1 setlinewidth
-solid
-0 1 1 edgecolor
-newpath 130 118.65 moveto
-140.47 117.01 lineto
-131.26 111.76 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-74 118.4 moveto 48 (RR: [6]) alignedtext
-grestore
-% CAA
-gsave
-0 0 0.75294 nodecolor
-newpath 1000 7 moveto
-1000 111 lineto
-1056 111 lineto
-1056 7 lineto
-closepath fill
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 1000 7 moveto
-1000 111 lineto
-1056 111 lineto
-1056 7 lineto
-closepath stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-1012.5 94.4 moveto 31 (CAA) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 1000 85 moveto
-1056 85 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-1009.5 68.4 moveto 37 (5':[5]) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 1000 59 moveto
-1056 59 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-1008 42.4 moveto 40 (~5':[]) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 1000 33 moveto
-1056 33 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-1016.5 16.4 moveto 23 (2.0) alignedtext
-grestore
-% AAA->CAA
-gsave
-1 setlinewidth
-0 1 1 edgecolor
-newpath 56.23 52.71 moveto
-85.36 47.72 132.19 41 173 41 curveto
-173 41 173 41 888 41 curveto
-922.66 41 961.75 46.49 989.8 51.41 curveto
-stroke
-0 1 1 edgecolor
-newpath 989.52 54.92 moveto
-999.98 53.26 lineto
-990.76 48.03 lineto
-closepath fill
-1 setlinewidth
-solid
-0 1 1 edgecolor
-newpath 989.52 54.92 moveto
-999.98 53.26 lineto
-990.76 48.03 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-504 46.4 moveto 48 (RR: [5]) alignedtext
-grestore
-% GAA->AAA
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 140.38 86.94 moveto
-134.64 82.35 128.42 78.15 122 75 curveto
-104.83 66.57 84.04 62.28 66.39 60.12 curveto
-stroke
-0 0 0 edgecolor
-newpath 66.72 56.64 moveto
-56.41 59.08 lineto
-65.99 63.6 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 66.72 56.64 moveto
-56.41 59.08 lineto
-65.99 63.6 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-75.5 80.4 moveto 45 (FF: [6]) alignedtext
-grestore
-% AGA
-gsave
-1 setlinewidth
-0 0 0 nodecolor
-newpath 290 80 moveto
-290 184 lineto
-346 184 lineto
-346 80 lineto
-closepath stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-302.5 167.4 moveto 31 (AGA) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 290 158 moveto
-346 158 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-304 141.4 moveto 28 (5':[]) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 290 132 moveto
-346 132 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-298 115.4 moveto 40 (~5':[]) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 290 106 moveto
-346 106 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-306.5 89.4 moveto 23 (1.0) alignedtext
-grestore
-% GAA->AGA
-gsave
-1 setlinewidth
-0 1 1 edgecolor
-newpath 205.55 127.51 moveto
-211.65 128.51 218 129.41 224 130 curveto
-242.3 131.8 262.69 132.4 279.79 132.51 curveto
-stroke
-0 1 1 edgecolor
-newpath 279.96 136.01 moveto
-289.96 132.53 lineto
-279.97 129.01 lineto
-closepath fill
-1 setlinewidth
-solid
-0 1 1 edgecolor
-newpath 279.96 136.01 moveto
-289.96 132.53 lineto
-279.97 129.01 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-224 137.4 moveto 48 (RR: [4]) alignedtext
-grestore
-% CAA->AAA
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 999.96 39.35 moveto
-972.68 22.19 929.41 0 888 0 curveto
-173 0 173 0 173 0 curveto
-134.1 0 93.26 18.22 64.87 34.23 curveto
-stroke
-0 0 0 edgecolor
-newpath 62.99 31.28 moveto
-56.11 39.33 lineto
-66.51 37.33 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 62.99 31.28 moveto
-56.11 39.33 lineto
-66.51 37.33 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-505.5 5.4 moveto 45 (FF: [5]) alignedtext
-grestore
-% ACA
-gsave
-1 setlinewidth
-0 0 0 nodecolor
-newpath 860 69 moveto
-860 173 lineto
-916 173 lineto
-916 69 lineto
-closepath stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-873 156.4 moveto 30 (ACA) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 860 147 moveto
-916 147 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-874 130.4 moveto 28 (5':[]) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 860 121 moveto
-916 121 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-868 104.4 moveto 40 (~5':[]) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 860 95 moveto
-916 95 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-876.5 78.4 moveto 23 (1.0) alignedtext
-grestore
-% CAA->ACA
-gsave
-1 setlinewidth
-0 1 1 edgecolor
-newpath 999.97 61.07 moveto
-980.57 63.41 954.63 68.4 934 79 curveto
-930.68 80.71 927.42 82.72 924.26 84.92 curveto
-stroke
-0 1 1 edgecolor
-newpath 921.98 82.26 moveto
-916.17 91.11 lineto
-926.24 87.81 lineto
-closepath fill
-1 setlinewidth
-solid
-0 1 1 edgecolor
-newpath 921.98 82.26 moveto
-916.17 91.11 lineto
-926.24 87.81 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-934 84.4 moveto 48 (RR: [3]) alignedtext
-grestore
-% ACA->CAA
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 916.3 117.12 moveto
-935.58 113.68 961.28 107.53 982 97 curveto
-985.29 95.33 988.55 93.39 991.73 91.29 curveto
-stroke
-0 0 0 edgecolor
-newpath 993.83 94.08 moveto
-999.92 85.41 lineto
-989.75 88.4 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 993.83 94.08 moveto
-999.92 85.41 lineto
-989.75 88.4 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-935.5 118.4 moveto 45 (FF: [3]) alignedtext
-grestore
-% AAC
-gsave
-0 0 0.75294 nodecolor
-newpath 720 74 moveto
-720 178 lineto
-776 178 lineto
-776 74 lineto
-closepath fill
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 720 74 moveto
-720 178 lineto
-776 178 lineto
-776 74 lineto
-closepath stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-732.5 161.4 moveto 31 (AAC) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 720 152 moveto
-776 152 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-729.5 135.4 moveto 37 (5':[3]) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 720 126 moveto
-776 126 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-728 109.4 moveto 40 (~5':[]) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 720 100 moveto
-776 100 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-736.5 83.4 moveto 23 (2.0) alignedtext
-grestore
-% ACA->AAC
-gsave
-1 setlinewidth
-0 1 1 edgecolor
-newpath 859.97 95.28 moveto
-854.37 91.47 848.28 88.12 842 86 curveto
-821.78 79.18 813.98 78.53 794 86 curveto
-790.73 87.22 787.54 88.8 784.46 90.61 curveto
-stroke
-0 1 1 edgecolor
-newpath 782.43 87.75 moveto
-776.11 96.25 lineto
-786.35 93.55 lineto
-closepath fill
-1 setlinewidth
-solid
-0 1 1 edgecolor
-newpath 782.43 87.75 moveto
-776.11 96.25 lineto
-786.35 93.55 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-794 91.4 moveto 48 (RR: [3]) alignedtext
-grestore
-% AGA->GAA
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 289.64 114.54 moveto
-283.98 111.84 277.95 109.46 272 108 curveto
-253.84 103.55 233.42 105.15 215.86 108.5 curveto
-stroke
-0 0 0 edgecolor
-newpath 214.93 105.12 moveto
-205.88 110.64 lineto
-216.4 111.97 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 214.93 105.12 moveto
-205.88 110.64 lineto
-216.4 111.97 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-225.5 113.4 moveto 45 (FF: [4]) alignedtext
+16.5 15.4 moveto 23 (1.0) alignedtext
grestore
% AAG
gsave
1 setlinewidth
0 0 0 nodecolor
-newpath 430 70 moveto
-430 174 lineto
-486 174 lineto
-486 70 lineto
+newpath 140 69 moveto
+140 173 lineto
+196 173 lineto
+196 69 lineto
closepath stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-442 157.4 moveto 32 (AAG) alignedtext
+152 156.4 moveto 32 (AAG) alignedtext
1 setlinewidth
0 0 0 nodecolor
-newpath 430 148 moveto
-486 148 lineto
+newpath 140 147 moveto
+196 147 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-444 131.4 moveto 28 (5':[]) alignedtext
+154 130.4 moveto 28 (5':[]) alignedtext
1 setlinewidth
0 0 0 nodecolor
-newpath 430 122 moveto
-486 122 lineto
+newpath 140 121 moveto
+196 121 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-438 105.4 moveto 40 (~5':[]) alignedtext
+148 104.4 moveto 40 (~5':[]) alignedtext
1 setlinewidth
0 0 0 nodecolor
-newpath 430 96 moveto
-486 96 lineto
+newpath 140 95 moveto
+196 95 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-446.5 79.4 moveto 23 (2.0) alignedtext
+156.5 78.4 moveto 23 (1.0) alignedtext
grestore
-% AGA->AAG
+% AAA->AAG
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 56 85.12 moveto
+61.65 89.58 67.77 93.78 74 97 curveto
+91.26 105.91 112.06 111.67 129.69 115.3 curveto
+stroke
+0 0 0 edgecolor
+newpath 129.18 118.76 moveto
+139.66 117.2 lineto
+130.49 111.89 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 129.18 118.76 moveto
+139.66 117.2 lineto
+130.49 111.89 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+75.5 118.4 moveto 45 (FF: [1]) alignedtext
+grestore
+% GAA
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1546 7 moveto
+1546 111 lineto
+1602 111 lineto
+1602 7 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1558 94.4 moveto 32 (GAA) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1546 85 moveto
+1602 85 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1560 68.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1546 59 moveto
+1602 59 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1554 42.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1546 33 moveto
+1602 33 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1562.5 16.4 moveto 23 (1.0) alignedtext
+grestore
+% AAA->GAA
gsave
1 setlinewidth
0 1 1 edgecolor
-newpath 346.33 129.98 moveto
-367.39 128.47 396.37 126.4 419.53 124.75 curveto
+newpath 56.03 52.57 moveto
+84.21 47.6 128.95 41 168 41 curveto
+168 41 168 41 1434 41 curveto
+1468.66 41 1507.75 46.49 1535.8 51.41 curveto
stroke
0 1 1 edgecolor
-newpath 419.99 128.22 moveto
-429.71 124.02 lineto
-419.49 121.24 lineto
+newpath 1535.52 54.92 moveto
+1545.98 53.26 lineto
+1536.76 48.03 lineto
closepath fill
1 setlinewidth
solid
0 1 1 edgecolor
-newpath 419.99 128.22 moveto
-429.71 124.02 lineto
-419.49 121.24 lineto
+newpath 1535.52 54.92 moveto
+1545.98 53.26 lineto
+1536.76 48.03 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-364 133.4 moveto 48 (RR: [4]) alignedtext
+772 46.4 moveto 48 (RR: [1]) alignedtext
grestore
-% TAA
+% AAG->AAA
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 139.99 87.84 moveto
+134.48 82.9 128.4 78.35 122 75 curveto
+104.93 66.06 83.99 61.74 66.21 59.68 curveto
+stroke
+0 1 1 edgecolor
+newpath 66.45 56.18 moveto
+56.16 58.71 lineto
+65.78 63.15 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 66.45 56.18 moveto
+56.16 58.71 lineto
+65.78 63.15 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+74 80.4 moveto 48 (RR: [1]) alignedtext
+grestore
+% AGG
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 280 88 moveto
+280 192 lineto
+336 192 lineto
+336 88 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+291.5 175.4 moveto 33 (AGG) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 280 166 moveto
+336 166 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+294 149.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 280 140 moveto
+336 140 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+288 123.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 280 114 moveto
+336 114 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+296.5 97.4 moveto 23 (1.0) alignedtext
+grestore
+% AAG->AGG
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 196.29 133.12 moveto
+202.05 135.11 208.14 136.89 214 138 curveto
+232.06 141.43 252.42 142.23 269.57 142.05 curveto
+stroke
+0 0 0 edgecolor
+newpath 269.86 145.54 moveto
+279.78 141.82 lineto
+269.7 138.54 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 269.86 145.54 moveto
+279.78 141.82 lineto
+269.7 138.54 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+215.5 147.4 moveto 45 (FF: [1]) alignedtext
+grestore
+% GAA->AAA
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 1545.96 39.35 moveto
+1518.68 22.19 1475.41 0 1434 0 curveto
+168 0 168 0 168 0 curveto
+130.89 0 92.17 17.61 64.88 33.42 curveto
+stroke
+0 0 0 edgecolor
+newpath 62.87 30.55 moveto
+56.09 38.69 lineto
+66.46 36.55 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 62.87 30.55 moveto
+56.09 38.69 lineto
+66.46 36.55 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+773.5 5.4 moveto 45 (FF: [1]) alignedtext
+grestore
+% CGA
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1406 69 moveto
+1406 173 lineto
+1462 173 lineto
+1462 69 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1418.5 156.4 moveto 31 (CGA) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1406 147 moveto
+1462 147 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1420 130.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1406 121 moveto
+1462 121 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1414 104.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1406 95 moveto
+1462 95 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1422.5 78.4 moveto 23 (1.0) alignedtext
+grestore
+% GAA->CGA
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 1545.97 61.07 moveto
+1526.57 63.41 1500.63 68.4 1480 79 curveto
+1476.68 80.71 1473.42 82.72 1470.26 84.92 curveto
+stroke
+0 1 1 edgecolor
+newpath 1467.98 82.26 moveto
+1462.17 91.11 lineto
+1472.24 87.81 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 1467.98 82.26 moveto
+1462.17 91.11 lineto
+1472.24 87.81 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+1480 84.4 moveto 48 (RR: [1]) alignedtext
+grestore
+% CGA->GAA
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 1462.3 117.12 moveto
+1481.58 113.68 1507.28 107.53 1528 97 curveto
+1531.29 95.33 1534.55 93.39 1537.73 91.29 curveto
+stroke
+0 0 0 edgecolor
+newpath 1539.83 94.08 moveto
+1545.92 85.41 lineto
+1535.75 88.4 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 1539.83 94.08 moveto
+1545.92 85.41 lineto
+1535.75 88.4 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+1481.5 118.4 moveto 45 (FF: [1]) alignedtext
+grestore
+% ACG
gsave
0 0 0.75294 nodecolor
-newpath 570 84 moveto
-570 188 lineto
-636 188 lineto
-636 84 lineto
+newpath 1256 70 moveto
+1256 174 lineto
+1322 174 lineto
+1322 70 lineto
closepath fill
1 setlinewidth
filled
0 0 0 nodecolor
-newpath 570 84 moveto
-570 188 lineto
-636 188 lineto
-636 84 lineto
+newpath 1256 70 moveto
+1256 174 lineto
+1322 174 lineto
+1322 70 lineto
closepath stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-588.5 171.4 moveto 29 (TAA) alignedtext
+1273.5 157.4 moveto 31 (ACG) alignedtext
1 setlinewidth
filled
0 0 0 nodecolor
-newpath 570 162 moveto
-636 162 lineto
+newpath 1256 148 moveto
+1322 148 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-578 145.4 moveto 50 (5':[2,1]) alignedtext
+1264 131.4 moveto 50 (5':[2,1]) alignedtext
1 setlinewidth
filled
0 0 0 nodecolor
-newpath 570 136 moveto
-636 136 lineto
+newpath 1256 122 moveto
+1322 122 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-583 119.4 moveto 40 (~5':[]) alignedtext
+1269 105.4 moveto 40 (~5':[]) alignedtext
1 setlinewidth
filled
0 0 0 nodecolor
-newpath 570 110 moveto
-636 110 lineto
+newpath 1256 96 moveto
+1322 96 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-591.5 93.4 moveto 23 (2.0) alignedtext
+1277.5 79.4 moveto 23 (2.0) alignedtext
grestore
-% TAA->AAG
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 569.84 109.98 moveto
-564.16 106.7 558.11 103.85 552 102 curveto
-531.58 95.82 524.89 97.66 504 102 curveto
-501.2 102.58 498.37 103.34 495.55 104.23 curveto
-stroke
-0 0 0 edgecolor
-newpath 494.33 100.95 moveto
-486.11 107.63 lineto
-496.71 107.53 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 494.33 100.95 moveto
-486.11 107.63 lineto
-496.71 107.53 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-505.5 107.4 moveto 45 (FF: [2]) alignedtext
-grestore
-% TAA->AAC
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 636.27 133.71 moveto
-658.16 132.2 686.89 130.21 709.74 128.64 curveto
-stroke
-0 0 0 edgecolor
-newpath 710.04 132.13 moveto
-719.77 127.95 lineto
-709.56 125.14 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 710.04 132.13 moveto
-719.77 127.95 lineto
-709.56 125.14 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-655.5 137.4 moveto 45 (FF: [1]) alignedtext
-grestore
-% AAG->AGA
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 429.83 108.35 moveto
-424.06 106.13 417.93 104.18 412 103 curveto
-391.07 98.85 384.5 97.08 364 103 curveto
-361.01 103.86 358.03 104.98 355.11 106.28 curveto
-stroke
-0 0 0 edgecolor
-newpath 353.32 103.27 moveto
-346.01 110.93 lineto
-356.51 109.5 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 353.32 103.27 moveto
-346.01 110.93 lineto
-356.51 109.5 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-365.5 108.4 moveto 45 (FF: [4]) alignedtext
-grestore
-% AAG->TAA
+% CGA->ACG
gsave
1 setlinewidth
0 1 1 edgecolor
-newpath 486.3 124.73 moveto
-507.19 126.75 536 129.53 559.77 131.83 curveto
+newpath 1405.8 91.99 moveto
+1400.31 87.9 1394.29 84.31 1388 82 curveto
+1367.97 74.65 1360.16 75.04 1340 82 curveto
+1336.92 83.07 1333.88 84.4 1330.91 85.94 curveto
stroke
0 1 1 edgecolor
-newpath 559.66 135.33 moveto
-569.95 132.81 lineto
-560.33 128.36 lineto
+newpath 1329.09 82.95 moveto
+1322.26 91.05 lineto
+1332.65 88.97 lineto
closepath fill
1 setlinewidth
solid
0 1 1 edgecolor
-newpath 559.66 135.33 moveto
-569.95 132.81 lineto
-560.33 128.36 lineto
+newpath 1329.09 82.95 moveto
+1322.26 91.05 lineto
+1332.65 88.97 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-504 136.4 moveto 48 (RR: [2]) alignedtext
+1340 87.4 moveto 48 (RR: [1]) alignedtext
grestore
-% AAC->ACA
+% CCA
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 558 73 moveto
+558 177 lineto
+614 177 lineto
+614 73 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+571 160.4 moveto 30 (CCA) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 558 151 moveto
+614 151 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+572 134.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 558 125 moveto
+614 125 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+566 108.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 558 99 moveto
+614 99 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+574.5 82.4 moveto 23 (1.0) alignedtext
+grestore
+% CAG
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 698 70 moveto
+698 174 lineto
+754 174 lineto
+754 70 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+710.5 157.4 moveto 31 (CAG) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 698 148 moveto
+754 148 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+712 131.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 698 122 moveto
+754 122 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+706 105.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 698 96 moveto
+754 96 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+714.5 79.4 moveto 23 (1.0) alignedtext
+grestore
+% CCA->CAG
gsave
1 setlinewidth
0 0 0 edgecolor
-newpath 776.33 124.99 moveto
-797.39 124.24 826.37 123.2 849.53 122.37 curveto
+newpath 614.33 124.39 moveto
+635.39 123.94 664.37 123.32 687.53 122.82 curveto
stroke
0 0 0 edgecolor
-newpath 849.84 125.87 moveto
-859.71 122.01 lineto
-849.59 118.87 lineto
+newpath 687.79 126.32 moveto
+697.71 122.61 lineto
+687.64 119.32 lineto
closepath fill
1 setlinewidth
solid
0 0 0 edgecolor
-newpath 849.84 125.87 moveto
-859.71 122.01 lineto
-849.59 118.87 lineto
+newpath 687.79 126.32 moveto
+697.71 122.61 lineto
+687.64 119.32 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-795.5 129.4 moveto 45 (FF: [3]) alignedtext
+633.5 128.4 moveto 45 (FF: [2]) alignedtext
grestore
-% AAC->TAA
+% GGA
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 420 78 moveto
+420 182 lineto
+476 182 lineto
+476 78 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+431.5 165.4 moveto 33 (GGA) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 420 156 moveto
+476 156 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+434 139.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 420 130 moveto
+476 130 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+428 113.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 420 104 moveto
+476 104 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+436.5 87.4 moveto 23 (2.0) alignedtext
+grestore
+% CCA->GGA
+gsave
+1 setlinewidth
+0.33333 1 1 edgecolor
+newpath 557.97 99.28 moveto
+552.37 95.47 546.28 92.12 540 90 curveto
+520.63 83.47 513.15 82.84 494 90 curveto
+490.73 91.22 487.54 92.8 484.46 94.61 curveto
+stroke
+0.33333 1 1 edgecolor
+newpath 482.43 91.75 moveto
+476.11 100.25 lineto
+486.35 97.55 lineto
+closepath fill
+1 setlinewidth
+solid
+0.33333 1 1 edgecolor
+newpath 482.43 91.75 moveto
+476.11 100.25 lineto
+486.35 97.55 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+494 95.4 moveto 46 (RF: [2]) alignedtext
+grestore
+% CAG->CCA
gsave
1 setlinewidth
0 1 1 edgecolor
-newpath 719.83 112.35 moveto
-714.06 110.13 707.93 108.18 702 107 curveto
-681.07 102.85 674.62 101.55 654 107 curveto
-651.18 107.74 648.36 108.68 645.57 109.77 curveto
+newpath 697.95 106.92 moveto
+692.17 104.47 686 102.31 680 101 curveto
+659.15 96.47 652.72 95.92 632 101 curveto
+629.21 101.68 626.4 102.57 623.63 103.6 curveto
stroke
0 1 1 edgecolor
-newpath 643.95 106.66 moveto
-636.24 113.92 lineto
-646.8 113.05 lineto
+newpath 622.19 100.4 moveto
+614.36 107.54 lineto
+624.93 106.84 lineto
closepath fill
1 setlinewidth
solid
0 1 1 edgecolor
-newpath 643.95 106.66 moveto
-636.24 113.92 lineto
-646.8 113.05 lineto
+newpath 622.19 100.4 moveto
+614.36 107.54 lineto
+624.93 106.84 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-654 112.4 moveto 48 (RR: [1]) alignedtext
+632 106.4 moveto 48 (RR: [2]) alignedtext
+grestore
+% AGC
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 838 88 moveto
+838 192 lineto
+894 192 lineto
+894 88 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+850.5 175.4 moveto 31 (AGC) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 838 166 moveto
+894 166 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+852 149.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 838 140 moveto
+894 140 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+846 123.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 838 114 moveto
+894 114 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+854.5 97.4 moveto 23 (1.0) alignedtext
+grestore
+% CAG->AGC
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 754.33 125.64 moveto
+775.39 128.35 804.37 132.08 827.53 135.05 curveto
+stroke
+0 0 0 edgecolor
+newpath 827.35 138.56 moveto
+837.71 136.36 lineto
+828.24 131.62 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 827.35 138.56 moveto
+837.71 136.36 lineto
+828.24 131.62 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+773.5 138.4 moveto 45 (FF: [2]) alignedtext
+grestore
+% GGA->CCA
+gsave
+1 setlinewidth
+0.33333 1 1 edgecolor
+newpath 476.26 128.98 moveto
+496.82 128.23 524.89 127.21 547.5 126.39 curveto
+stroke
+0.33333 1 1 edgecolor
+newpath 547.91 129.88 moveto
+557.78 126.02 lineto
+547.66 122.89 lineto
+closepath fill
+1 setlinewidth
+solid
+0.33333 1 1 edgecolor
+newpath 547.91 129.88 moveto
+557.78 126.02 lineto
+547.66 122.89 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+494 133.4 moveto 46 (RF: [2]) alignedtext
+grestore
+% GGA->AGG
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 419.82 108.07 moveto
+414.19 104.74 408.12 101.82 402 100 curveto
+381.55 93.92 373.98 92.53 354 100 curveto
+350.73 101.22 347.54 102.8 344.46 104.61 curveto
+stroke
+0 1 1 edgecolor
+newpath 342.43 101.75 moveto
+336.11 110.25 lineto
+346.35 107.55 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 342.43 101.75 moveto
+336.11 110.25 lineto
+346.35 107.55 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+354 105.4 moveto 48 (RR: [1]) alignedtext
+grestore
+% ACG->CGA
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 1322.27 121.77 moveto
+1344.16 121.62 1372.89 121.42 1395.74 121.26 curveto
+stroke
+0 0 0 edgecolor
+newpath 1395.8 124.76 moveto
+1405.77 121.19 lineto
+1395.75 117.76 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 1395.8 124.76 moveto
+1405.77 121.19 lineto
+1395.75 117.76 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+1341.5 126.4 moveto 45 (FF: [1]) alignedtext
+grestore
+% CCG
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1118 73 moveto
+1118 177 lineto
+1174 177 lineto
+1174 73 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1130.5 160.4 moveto 31 (CCG) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1118 151 moveto
+1174 151 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1132 134.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1118 125 moveto
+1174 125 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1126 108.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1118 99 moveto
+1174 99 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1134.5 82.4 moveto 23 (1.0) alignedtext
+grestore
+% ACG->CCG
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 1255.78 93.53 moveto
+1250.16 90.03 1244.14 86.99 1238 85 curveto
+1218.55 78.69 1211.15 77.84 1192 85 curveto
+1188.73 86.22 1185.54 87.8 1182.46 89.61 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 1180.43 86.75 moveto
+1174.11 95.25 lineto
+1184.35 92.55 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 1180.43 86.75 moveto
+1174.11 95.25 lineto
+1184.35 92.55 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+1192 90.4 moveto 46 (FR: [2]) alignedtext
+grestore
+% AGG->AAG
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 279.64 122.54 moveto
+273.98 119.84 267.95 117.46 262 116 curveto
+244.12 111.62 223.78 112.06 206.61 113.93 curveto
+stroke
+0 1 1 edgecolor
+newpath 205.84 110.5 moveto
+196.37 115.25 lineto
+206.74 117.44 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 205.84 110.5 moveto
+196.37 115.25 lineto
+206.74 117.44 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+214 121.4 moveto 48 (RR: [1]) alignedtext
+grestore
+% AGG->GGA
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 336.33 137.98 moveto
+357.39 136.47 386.37 134.4 409.53 132.75 curveto
+stroke
+0 0 0 edgecolor
+newpath 409.99 136.22 moveto
+419.71 132.02 lineto
+409.49 129.24 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 409.99 136.22 moveto
+419.71 132.02 lineto
+409.49 129.24 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+355.5 141.4 moveto 45 (FF: [1]) alignedtext
+grestore
+% GCC
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 978 78 moveto
+978 182 lineto
+1034 182 lineto
+1034 78 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+990.5 165.4 moveto 31 (GCC) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 978 156 moveto
+1034 156 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+992 139.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 978 130 moveto
+1034 130 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+986 113.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 978 104 moveto
+1034 104 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+994.5 87.4 moveto 23 (1.0) alignedtext
+grestore
+% GCC->CCG
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 1034.33 128.99 moveto
+1055.39 128.24 1084.37 127.2 1107.53 126.37 curveto
+stroke
+0 0 0 edgecolor
+newpath 1107.84 129.87 moveto
+1117.71 126.01 lineto
+1107.59 122.87 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 1107.84 129.87 moveto
+1117.71 126.01 lineto
+1107.59 122.87 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+1053.5 133.4 moveto 45 (FF: [2]) alignedtext
+grestore
+% GCC->AGC
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 977.82 108.07 moveto
+972.19 104.74 966.12 101.82 960 100 curveto
+939.55 93.92 931.98 92.53 912 100 curveto
+908.73 101.22 905.54 102.8 902.46 104.61 curveto
+stroke
+0 1 1 edgecolor
+newpath 900.43 101.75 moveto
+894.11 110.25 lineto
+904.35 107.55 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 900.43 101.75 moveto
+894.11 110.25 lineto
+904.35 107.55 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+912 105.4 moveto 48 (RR: [2]) alignedtext
+grestore
+% CCG->ACG
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 1174.25 124.41 moveto
+1194.58 123.98 1222.38 123.4 1245.53 122.91 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 1245.86 126.41 moveto
+1255.79 122.7 lineto
+1245.72 119.41 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 1245.86 126.41 moveto
+1255.79 122.7 lineto
+1245.72 119.41 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+1192 129.4 moveto 46 (FR: [2]) alignedtext
+grestore
+% CCG->GCC
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 1117.95 109.92 moveto
+1112.17 107.47 1106 105.31 1100 104 curveto
+1079.15 99.47 1072.63 98.57 1052 104 curveto
+1049.17 104.74 1046.34 105.71 1043.54 106.82 curveto
+stroke
+0 1 1 edgecolor
+newpath 1041.85 103.74 moveto
+1034.23 111.1 lineto
+1044.77 110.1 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 1041.85 103.74 moveto
+1034.23 111.1 lineto
+1044.77 110.1 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+1052 109.4 moveto 48 (RR: [2]) alignedtext
+grestore
+% AGC->CAG
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 837.97 111.91 moveto
+832.42 107.85 826.34 104.28 820 102 curveto
+799.93 94.78 792.89 97.66 772 102 curveto
+769.2 102.58 766.37 103.34 763.55 104.23 curveto
+stroke
+0 1 1 edgecolor
+newpath 762.33 100.95 moveto
+754.11 107.63 lineto
+764.71 107.53 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 762.33 100.95 moveto
+754.11 107.63 lineto
+764.71 107.53 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+772 107.4 moveto 48 (RR: [2]) alignedtext
+grestore
+% AGC->GCC
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 894.33 137.98 moveto
+915.39 136.47 944.37 134.4 967.53 132.75 curveto
+stroke
+0 0 0 edgecolor
+newpath 967.99 136.22 moveto
+977.71 132.02 lineto
+967.49 129.24 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 967.99 136.22 moveto
+977.71 132.02 lineto
+967.49 129.24 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+913.5 141.4 moveto 45 (FF: [2]) alignedtext
grestore
endpage
showpage
@@ -913,7 +1223,7 @@
%%EndPage: 1
%%Trailer
%%Pages: 1
-%%BoundingBox: 36 36 1100 232
+%%BoundingBox: 36 36 1646 236
end
restore
%%EOF
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoR/..binmerge.crc b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoR/..binmerge.crc
index 4b9875e..c2a29c5 100644
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoR/..binmerge.crc
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoR/..binmerge.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoR/.binmerge b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoR/.binmerge
index b3b88cd..c49abaa 100755
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoR/.binmerge
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoR/.binmerge
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoR/bin/.part-00000.crc b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoR/bin/.part-00000.crc
index 7bbc056..8034a50 100644
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoR/bin/.part-00000.crc
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoR/bin/.part-00000.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoR/bin/part-00000 b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoR/bin/part-00000
index 4ef1a22..280855e 100755
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoR/bin/part-00000
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoR/bin/part-00000
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoR/data b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoR/data
index 0b23e6e..e2a8a3c 100644
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoR/data
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoR/data
@@ -1,8 +1,12 @@
-AAA {[] [] [] [{GAA:[6]}, {CAA:[5]}] {5':[], ~5':[(5-0_0),(6-0_0)]} 2.0x}
-CAA {[{AAA:[5]}] [] [] [{ACA:[3]}] {5':[], ~5':[]} 2.0x}
-GAA {[{AAA:[6]}] [] [] [{AGA:[4]}] {5':[], ~5':[(4-0_0)]} 2.0x}
-TAA {[{AAG:[2]}, {AAC:[1]}] [] [] [] {5':[(2-0_0),(1-0_0)], ~5':[]} 2.0x}
-ACA {[{CAA:[3]}] [] [] [{AAC:[3]}] {5':[], ~5':[]} 1.0x}
-AGA {[{GAA:[4]}] [] [] [{AAG:[4]}] {5':[], ~5':[]} 1.0x}
-AAC {[{ACA:[3]}] [] [] [{TAA:[1]}] {5':[(3-0_0)], ~5':[]} 2.0x}
-AAG {[{AGA:[4]}] [] [] [{TAA:[2]}] {5':[], ~5':[]} 2.0x}
+AAA {[{AAG:[1]}] [] [] [{GAA:[1]}] {5':[], ~5':[]} 1.0x}
+GAA {[{AAA:[1]}] [] [] [{CGA:[1]}] {5':[], ~5':[]} 1.0x}
+CCA {[{CAG:[2]}] [] [] [{ACC:[2]}] {5':[], ~5':[]} 1.0x}
+CGA {[{GAA:[1]}] [] [] [{ACG:[1]}] {5':[], ~5':[]} 1.0x}
+ACC {[{CCA:[2]}] [{AGG:[1]}] [] [] {5':[], ~5':[]} 2.0x}
+GCC {[{CCG:[2]}] [] [] [{AGC:[2]}] {5':[], ~5':[]} 1.0x}
+AGC {[{GCC:[2]}] [] [] [{CAG:[2]}] {5':[], ~5':[]} 1.0x}
+AAG {[{AGG:[1]}] [] [] [{AAA:[1]}] {5':[], ~5':[]} 1.0x}
+CAG {[{AGC:[2]}] [] [] [{CCA:[2]}] {5':[], ~5':[]} 1.0x}
+ACG {[{CGA:[1]}] [{CCG:[2]}] [] [] {5':[(2-0_0),(1-0_0)], ~5':[]} 2.0x}
+CCG {[] [{ACG:[2]}] [] [{GCC:[2]}] {5':[], ~5':[]} 1.0x}
+AGG {[] [{ACC:[1]}] [] [{AAG:[1]}] {5':[], ~5':[]} 1.0x}
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoR/graphviz/result.ps b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoR/graphviz/result.ps
index f9b4df8..7936784 100644
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoR/graphviz/result.ps
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/LtoR/graphviz/result.ps
@@ -178,733 +178,1043 @@
%%EndSetup
setupLatin1
%%Page: 1 1
-%%PageBoundingBox: 36 36 1122 232
+%%PageBoundingBox: 36 36 1646 236
%%PageOrientation: Portrait
0 0 1 beginpage
gsave
-36 36 1086 196 boxprim clip newpath
+36 36 1610 200 boxprim clip newpath
1 1 set_scale 0 rotate 40 41 translate
% AAA
gsave
-0 0 0.75294 nodecolor
-newpath 0 6 moveto
-0 110 lineto
-78 110 lineto
-78 6 lineto
-closepath fill
1 setlinewidth
-filled
0 0 0 nodecolor
newpath 0 6 moveto
0 110 lineto
-78 110 lineto
-78 6 lineto
+56 110 lineto
+56 6 lineto
closepath stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-23.5 93.4 moveto 31 (AAA) alignedtext
+12.5 93.4 moveto 31 (AAA) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
newpath 0 84 moveto
-78 84 lineto
+56 84 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-25 67.4 moveto 28 (5':[]) alignedtext
+14 67.4 moveto 28 (5':[]) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
newpath 0 58 moveto
-78 58 lineto
+56 58 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-8 41.4 moveto 62 (~5':[5,6]) alignedtext
+8 41.4 moveto 40 (~5':[]) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
newpath 0 32 moveto
-78 32 lineto
+56 32 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-27.5 15.4 moveto 23 (2.0) alignedtext
-grestore
-% GAA
-gsave
-0 0 0.75294 nodecolor
-newpath 162.5 69 moveto
-162.5 173 lineto
-227.5 173 lineto
-227.5 69 lineto
-closepath fill
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 162.5 69 moveto
-162.5 173 lineto
-227.5 173 lineto
-227.5 69 lineto
-closepath stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-179 156.4 moveto 32 (GAA) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 162.5 147 moveto
-227.5 147 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-181 130.4 moveto 28 (5':[]) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 162.5 121 moveto
-227.5 121 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-170.5 104.4 moveto 49 (~5':[4]) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 162.5 95 moveto
-227.5 95 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-183.5 78.4 moveto 23 (2.0) alignedtext
-grestore
-% AAA->GAA
-gsave
-1 setlinewidth
-0 1 1 edgecolor
-newpath 78.1 87.41 moveto
-83.91 90.99 89.98 94.32 96 97 curveto
-113.77 104.92 134.56 110.46 152.48 114.21 curveto
-stroke
-0 1 1 edgecolor
-newpath 151.89 117.66 moveto
-162.38 116.16 lineto
-153.24 110.79 lineto
-closepath fill
-1 setlinewidth
-solid
-0 1 1 edgecolor
-newpath 151.89 117.66 moveto
-162.38 116.16 lineto
-153.24 110.79 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-96 117.4 moveto 48 (RR: [6]) alignedtext
-grestore
-% CAA
-gsave
-1 setlinewidth
-0 0 0 nodecolor
-newpath 1022 7 moveto
-1022 111 lineto
-1078 111 lineto
-1078 7 lineto
-closepath stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-1034.5 94.4 moveto 31 (CAA) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 1022 85 moveto
-1078 85 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-1036 68.4 moveto 28 (5':[]) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 1022 59 moveto
-1078 59 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-1030 42.4 moveto 40 (~5':[]) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 1022 33 moveto
-1078 33 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-1038.5 16.4 moveto 23 (2.0) alignedtext
-grestore
-% AAA->CAA
-gsave
-1 setlinewidth
-0 1 1 edgecolor
-newpath 78.3 51.33 moveto
-109.77 46.57 155.09 41 195 41 curveto
-195 41 195 41 910 41 curveto
-944.66 41 983.75 46.49 1011.8 51.41 curveto
-stroke
-0 1 1 edgecolor
-newpath 1011.52 54.92 moveto
-1021.98 53.26 lineto
-1012.76 48.03 lineto
-closepath fill
-1 setlinewidth
-solid
-0 1 1 edgecolor
-newpath 1011.52 54.92 moveto
-1021.98 53.26 lineto
-1012.76 48.03 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-526 46.4 moveto 48 (RR: [5]) alignedtext
-grestore
-% GAA->AAA
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 162.44 86.84 moveto
-156.68 82.26 150.45 78.09 144 75 curveto
-126.87 66.78 106.55 62.43 88.37 60.15 curveto
-stroke
-0 0 0 edgecolor
-newpath 88.56 56.65 moveto
-78.24 59.07 lineto
-87.81 63.61 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 88.56 56.65 moveto
-78.24 59.07 lineto
-87.81 63.61 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-97.5 80.4 moveto 45 (FF: [6]) alignedtext
-grestore
-% AGA
-gsave
-1 setlinewidth
-0 0 0 nodecolor
-newpath 312 80 moveto
-312 184 lineto
-368 184 lineto
-368 80 lineto
-closepath stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-324.5 167.4 moveto 31 (AGA) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 312 158 moveto
-368 158 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-326 141.4 moveto 28 (5':[]) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 312 132 moveto
-368 132 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-320 115.4 moveto 40 (~5':[]) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 312 106 moveto
-368 106 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-328.5 89.4 moveto 23 (1.0) alignedtext
-grestore
-% GAA->AGA
-gsave
-1 setlinewidth
-0 1 1 edgecolor
-newpath 227.55 127.51 moveto
-233.65 128.51 240 129.41 246 130 curveto
-264.3 131.8 284.69 132.4 301.79 132.51 curveto
-stroke
-0 1 1 edgecolor
-newpath 301.96 136.01 moveto
-311.96 132.53 lineto
-301.97 129.01 lineto
-closepath fill
-1 setlinewidth
-solid
-0 1 1 edgecolor
-newpath 301.96 136.01 moveto
-311.96 132.53 lineto
-301.97 129.01 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-246 137.4 moveto 48 (RR: [4]) alignedtext
-grestore
-% CAA->AAA
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 1021.96 39.35 moveto
-994.68 22.19 951.41 0 910 0 curveto
-195 0 195 0 195 0 curveto
-157.16 0 117.21 15.18 87.22 30 curveto
-stroke
-0 0 0 edgecolor
-newpath 85.56 26.92 moveto
-78.24 34.58 lineto
-88.74 33.16 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 85.56 26.92 moveto
-78.24 34.58 lineto
-88.74 33.16 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-527.5 5.4 moveto 45 (FF: [5]) alignedtext
-grestore
-% ACA
-gsave
-1 setlinewidth
-0 0 0 nodecolor
-newpath 882 69 moveto
-882 173 lineto
-938 173 lineto
-938 69 lineto
-closepath stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-895 156.4 moveto 30 (ACA) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 882 147 moveto
-938 147 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-896 130.4 moveto 28 (5':[]) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 882 121 moveto
-938 121 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-890 104.4 moveto 40 (~5':[]) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 882 95 moveto
-938 95 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-898.5 78.4 moveto 23 (1.0) alignedtext
-grestore
-% CAA->ACA
-gsave
-1 setlinewidth
-0 1 1 edgecolor
-newpath 1021.97 61.07 moveto
-1002.57 63.41 976.63 68.4 956 79 curveto
-952.68 80.71 949.42 82.72 946.26 84.92 curveto
-stroke
-0 1 1 edgecolor
-newpath 943.98 82.26 moveto
-938.17 91.11 lineto
-948.24 87.81 lineto
-closepath fill
-1 setlinewidth
-solid
-0 1 1 edgecolor
-newpath 943.98 82.26 moveto
-938.17 91.11 lineto
-948.24 87.81 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-956 84.4 moveto 48 (RR: [3]) alignedtext
-grestore
-% ACA->CAA
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 938.3 117.12 moveto
-957.58 113.68 983.28 107.53 1004 97 curveto
-1007.29 95.33 1010.55 93.39 1013.73 91.29 curveto
-stroke
-0 0 0 edgecolor
-newpath 1015.83 94.08 moveto
-1021.92 85.41 lineto
-1011.75 88.4 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 1015.83 94.08 moveto
-1021.92 85.41 lineto
-1011.75 88.4 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-957.5 118.4 moveto 45 (FF: [3]) alignedtext
-grestore
-% AAC
-gsave
-0 0 0.75294 nodecolor
-newpath 742 74 moveto
-742 178 lineto
-798 178 lineto
-798 74 lineto
-closepath fill
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 742 74 moveto
-742 178 lineto
-798 178 lineto
-798 74 lineto
-closepath stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-754.5 161.4 moveto 31 (AAC) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 742 152 moveto
-798 152 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-751.5 135.4 moveto 37 (5':[3]) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 742 126 moveto
-798 126 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-750 109.4 moveto 40 (~5':[]) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 742 100 moveto
-798 100 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-758.5 83.4 moveto 23 (2.0) alignedtext
-grestore
-% ACA->AAC
-gsave
-1 setlinewidth
-0 1 1 edgecolor
-newpath 881.97 95.28 moveto
-876.37 91.47 870.28 88.12 864 86 curveto
-843.78 79.18 835.98 78.53 816 86 curveto
-812.73 87.22 809.54 88.8 806.46 90.61 curveto
-stroke
-0 1 1 edgecolor
-newpath 804.43 87.75 moveto
-798.11 96.25 lineto
-808.35 93.55 lineto
-closepath fill
-1 setlinewidth
-solid
-0 1 1 edgecolor
-newpath 804.43 87.75 moveto
-798.11 96.25 lineto
-808.35 93.55 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-816 91.4 moveto 48 (RR: [3]) alignedtext
-grestore
-% AGA->GAA
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 311.64 114.54 moveto
-305.98 111.84 299.95 109.46 294 108 curveto
-275.84 103.55 255.42 105.15 237.86 108.5 curveto
-stroke
-0 0 0 edgecolor
-newpath 236.93 105.12 moveto
-227.88 110.64 lineto
-238.4 111.97 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 236.93 105.12 moveto
-227.88 110.64 lineto
-238.4 111.97 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-247.5 113.4 moveto 45 (FF: [4]) alignedtext
+16.5 15.4 moveto 23 (1.0) alignedtext
grestore
% AAG
gsave
1 setlinewidth
0 0 0 nodecolor
-newpath 452 70 moveto
-452 174 lineto
-508 174 lineto
-508 70 lineto
+newpath 140 69 moveto
+140 173 lineto
+196 173 lineto
+196 69 lineto
closepath stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-464 157.4 moveto 32 (AAG) alignedtext
+152 156.4 moveto 32 (AAG) alignedtext
1 setlinewidth
0 0 0 nodecolor
-newpath 452 148 moveto
-508 148 lineto
+newpath 140 147 moveto
+196 147 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-466 131.4 moveto 28 (5':[]) alignedtext
+154 130.4 moveto 28 (5':[]) alignedtext
1 setlinewidth
0 0 0 nodecolor
-newpath 452 122 moveto
-508 122 lineto
+newpath 140 121 moveto
+196 121 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-460 105.4 moveto 40 (~5':[]) alignedtext
+148 104.4 moveto 40 (~5':[]) alignedtext
1 setlinewidth
0 0 0 nodecolor
-newpath 452 96 moveto
-508 96 lineto
+newpath 140 95 moveto
+196 95 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-468.5 79.4 moveto 23 (2.0) alignedtext
+156.5 78.4 moveto 23 (1.0) alignedtext
grestore
-% AGA->AAG
+% AAA->AAG
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 56 85.12 moveto
+61.65 89.58 67.77 93.78 74 97 curveto
+91.26 105.91 112.06 111.67 129.69 115.3 curveto
+stroke
+0 0 0 edgecolor
+newpath 129.18 118.76 moveto
+139.66 117.2 lineto
+130.49 111.89 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 129.18 118.76 moveto
+139.66 117.2 lineto
+130.49 111.89 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+75.5 118.4 moveto 45 (FF: [1]) alignedtext
+grestore
+% GAA
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1546 7 moveto
+1546 111 lineto
+1602 111 lineto
+1602 7 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1558 94.4 moveto 32 (GAA) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1546 85 moveto
+1602 85 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1560 68.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1546 59 moveto
+1602 59 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1554 42.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1546 33 moveto
+1602 33 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1562.5 16.4 moveto 23 (1.0) alignedtext
+grestore
+% AAA->GAA
gsave
1 setlinewidth
0 1 1 edgecolor
-newpath 368.33 129.98 moveto
-389.39 128.47 418.37 126.4 441.53 124.75 curveto
+newpath 56.03 52.57 moveto
+84.21 47.6 128.95 41 168 41 curveto
+168 41 168 41 1434 41 curveto
+1468.66 41 1507.75 46.49 1535.8 51.41 curveto
stroke
0 1 1 edgecolor
-newpath 441.99 128.22 moveto
-451.71 124.02 lineto
-441.49 121.24 lineto
+newpath 1535.52 54.92 moveto
+1545.98 53.26 lineto
+1536.76 48.03 lineto
closepath fill
1 setlinewidth
solid
0 1 1 edgecolor
-newpath 441.99 128.22 moveto
-451.71 124.02 lineto
-441.49 121.24 lineto
+newpath 1535.52 54.92 moveto
+1545.98 53.26 lineto
+1536.76 48.03 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-386 133.4 moveto 48 (RR: [4]) alignedtext
+772 46.4 moveto 48 (RR: [1]) alignedtext
grestore
-% TAA
+% AAG->AAA
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 139.99 87.84 moveto
+134.48 82.9 128.4 78.35 122 75 curveto
+104.93 66.06 83.99 61.74 66.21 59.68 curveto
+stroke
+0 1 1 edgecolor
+newpath 66.45 56.18 moveto
+56.16 58.71 lineto
+65.78 63.15 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 66.45 56.18 moveto
+56.16 58.71 lineto
+65.78 63.15 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+74 80.4 moveto 48 (RR: [1]) alignedtext
+grestore
+% AGG
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 280 88 moveto
+280 192 lineto
+336 192 lineto
+336 88 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+291.5 175.4 moveto 33 (AGG) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 280 166 moveto
+336 166 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+294 149.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 280 140 moveto
+336 140 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+288 123.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 280 114 moveto
+336 114 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+296.5 97.4 moveto 23 (1.0) alignedtext
+grestore
+% AAG->AGG
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 196.29 133.12 moveto
+202.05 135.11 208.14 136.89 214 138 curveto
+232.06 141.43 252.42 142.23 269.57 142.05 curveto
+stroke
+0 0 0 edgecolor
+newpath 269.86 145.54 moveto
+279.78 141.82 lineto
+269.7 138.54 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 269.86 145.54 moveto
+279.78 141.82 lineto
+269.7 138.54 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+215.5 147.4 moveto 45 (FF: [1]) alignedtext
+grestore
+% GAA->AAA
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 1545.96 39.35 moveto
+1518.68 22.19 1475.41 0 1434 0 curveto
+168 0 168 0 168 0 curveto
+130.89 0 92.17 17.61 64.88 33.42 curveto
+stroke
+0 0 0 edgecolor
+newpath 62.87 30.55 moveto
+56.09 38.69 lineto
+66.46 36.55 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 62.87 30.55 moveto
+56.09 38.69 lineto
+66.46 36.55 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+773.5 5.4 moveto 45 (FF: [1]) alignedtext
+grestore
+% CGA
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1406 69 moveto
+1406 173 lineto
+1462 173 lineto
+1462 69 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1418.5 156.4 moveto 31 (CGA) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1406 147 moveto
+1462 147 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1420 130.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1406 121 moveto
+1462 121 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1414 104.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1406 95 moveto
+1462 95 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1422.5 78.4 moveto 23 (1.0) alignedtext
+grestore
+% GAA->CGA
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 1545.97 61.07 moveto
+1526.57 63.41 1500.63 68.4 1480 79 curveto
+1476.68 80.71 1473.42 82.72 1470.26 84.92 curveto
+stroke
+0 1 1 edgecolor
+newpath 1467.98 82.26 moveto
+1462.17 91.11 lineto
+1472.24 87.81 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 1467.98 82.26 moveto
+1462.17 91.11 lineto
+1472.24 87.81 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+1480 84.4 moveto 48 (RR: [1]) alignedtext
+grestore
+% CGA->GAA
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 1462.3 117.12 moveto
+1481.58 113.68 1507.28 107.53 1528 97 curveto
+1531.29 95.33 1534.55 93.39 1537.73 91.29 curveto
+stroke
+0 0 0 edgecolor
+newpath 1539.83 94.08 moveto
+1545.92 85.41 lineto
+1535.75 88.4 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 1539.83 94.08 moveto
+1545.92 85.41 lineto
+1535.75 88.4 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+1481.5 118.4 moveto 45 (FF: [1]) alignedtext
+grestore
+% ACG
gsave
0 0 0.75294 nodecolor
-newpath 592 84 moveto
-592 188 lineto
-658 188 lineto
-658 84 lineto
+newpath 1256 70 moveto
+1256 174 lineto
+1322 174 lineto
+1322 70 lineto
closepath fill
1 setlinewidth
filled
0 0 0 nodecolor
-newpath 592 84 moveto
-592 188 lineto
-658 188 lineto
-658 84 lineto
+newpath 1256 70 moveto
+1256 174 lineto
+1322 174 lineto
+1322 70 lineto
closepath stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-610.5 171.4 moveto 29 (TAA) alignedtext
+1273.5 157.4 moveto 31 (ACG) alignedtext
1 setlinewidth
filled
0 0 0 nodecolor
-newpath 592 162 moveto
-658 162 lineto
+newpath 1256 148 moveto
+1322 148 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-600 145.4 moveto 50 (5':[2,1]) alignedtext
+1264 131.4 moveto 50 (5':[2,1]) alignedtext
1 setlinewidth
filled
0 0 0 nodecolor
-newpath 592 136 moveto
-658 136 lineto
+newpath 1256 122 moveto
+1322 122 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-605 119.4 moveto 40 (~5':[]) alignedtext
+1269 105.4 moveto 40 (~5':[]) alignedtext
1 setlinewidth
filled
0 0 0 nodecolor
-newpath 592 110 moveto
-658 110 lineto
+newpath 1256 96 moveto
+1322 96 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-613.5 93.4 moveto 23 (2.0) alignedtext
+1277.5 79.4 moveto 23 (2.0) alignedtext
grestore
-% TAA->AAG
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 591.84 109.98 moveto
-586.16 106.7 580.11 103.85 574 102 curveto
-553.58 95.82 546.89 97.66 526 102 curveto
-523.2 102.58 520.37 103.34 517.55 104.23 curveto
-stroke
-0 0 0 edgecolor
-newpath 516.33 100.95 moveto
-508.11 107.63 lineto
-518.71 107.53 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 516.33 100.95 moveto
-508.11 107.63 lineto
-518.71 107.53 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-527.5 107.4 moveto 45 (FF: [2]) alignedtext
-grestore
-% TAA->AAC
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 658.27 133.71 moveto
-680.16 132.2 708.89 130.21 731.74 128.64 curveto
-stroke
-0 0 0 edgecolor
-newpath 732.04 132.13 moveto
-741.77 127.95 lineto
-731.56 125.14 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 732.04 132.13 moveto
-741.77 127.95 lineto
-731.56 125.14 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-677.5 137.4 moveto 45 (FF: [1]) alignedtext
-grestore
-% AAG->AGA
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 451.83 108.35 moveto
-446.06 106.13 439.93 104.18 434 103 curveto
-413.07 98.85 406.5 97.08 386 103 curveto
-383.01 103.86 380.03 104.98 377.11 106.28 curveto
-stroke
-0 0 0 edgecolor
-newpath 375.32 103.27 moveto
-368.01 110.93 lineto
-378.51 109.5 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 375.32 103.27 moveto
-368.01 110.93 lineto
-378.51 109.5 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-387.5 108.4 moveto 45 (FF: [4]) alignedtext
-grestore
-% AAG->TAA
+% CGA->ACG
gsave
1 setlinewidth
0 1 1 edgecolor
-newpath 508.3 124.73 moveto
-529.19 126.75 558 129.53 581.77 131.83 curveto
+newpath 1405.8 91.99 moveto
+1400.31 87.9 1394.29 84.31 1388 82 curveto
+1367.97 74.65 1360.16 75.04 1340 82 curveto
+1336.92 83.07 1333.88 84.4 1330.91 85.94 curveto
stroke
0 1 1 edgecolor
-newpath 581.66 135.33 moveto
-591.95 132.81 lineto
-582.33 128.36 lineto
+newpath 1329.09 82.95 moveto
+1322.26 91.05 lineto
+1332.65 88.97 lineto
closepath fill
1 setlinewidth
solid
0 1 1 edgecolor
-newpath 581.66 135.33 moveto
-591.95 132.81 lineto
-582.33 128.36 lineto
+newpath 1329.09 82.95 moveto
+1322.26 91.05 lineto
+1332.65 88.97 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-526 136.4 moveto 48 (RR: [2]) alignedtext
+1340 87.4 moveto 48 (RR: [1]) alignedtext
grestore
-% AAC->ACA
+% CCA
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 558 73 moveto
+558 177 lineto
+614 177 lineto
+614 73 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+571 160.4 moveto 30 (CCA) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 558 151 moveto
+614 151 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+572 134.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 558 125 moveto
+614 125 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+566 108.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 558 99 moveto
+614 99 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+574.5 82.4 moveto 23 (1.0) alignedtext
+grestore
+% CAG
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 698 70 moveto
+698 174 lineto
+754 174 lineto
+754 70 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+710.5 157.4 moveto 31 (CAG) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 698 148 moveto
+754 148 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+712 131.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 698 122 moveto
+754 122 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+706 105.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 698 96 moveto
+754 96 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+714.5 79.4 moveto 23 (1.0) alignedtext
+grestore
+% CCA->CAG
gsave
1 setlinewidth
0 0 0 edgecolor
-newpath 798.33 124.99 moveto
-819.39 124.24 848.37 123.2 871.53 122.37 curveto
+newpath 614.33 124.39 moveto
+635.39 123.94 664.37 123.32 687.53 122.82 curveto
stroke
0 0 0 edgecolor
-newpath 871.84 125.87 moveto
-881.71 122.01 lineto
-871.59 118.87 lineto
+newpath 687.79 126.32 moveto
+697.71 122.61 lineto
+687.64 119.32 lineto
closepath fill
1 setlinewidth
solid
0 0 0 edgecolor
-newpath 871.84 125.87 moveto
-881.71 122.01 lineto
-871.59 118.87 lineto
+newpath 687.79 126.32 moveto
+697.71 122.61 lineto
+687.64 119.32 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-817.5 129.4 moveto 45 (FF: [3]) alignedtext
+633.5 128.4 moveto 45 (FF: [2]) alignedtext
grestore
-% AAC->TAA
+% ACC
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 418 78 moveto
+418 182 lineto
+474 182 lineto
+474 78 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+431 165.4 moveto 30 (ACC) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 418 156 moveto
+474 156 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+432 139.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 418 130 moveto
+474 130 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+426 113.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 418 104 moveto
+474 104 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+434.5 87.4 moveto 23 (2.0) alignedtext
+grestore
+% CCA->ACC
gsave
1 setlinewidth
0 1 1 edgecolor
-newpath 741.83 112.35 moveto
-736.06 110.13 729.93 108.18 724 107 curveto
-703.07 102.85 696.62 101.55 676 107 curveto
-673.18 107.74 670.36 108.68 667.57 109.77 curveto
+newpath 557.97 99.28 moveto
+552.37 95.47 546.28 92.12 540 90 curveto
+519.78 83.18 511.98 82.53 492 90 curveto
+488.73 91.22 485.54 92.8 482.46 94.61 curveto
stroke
0 1 1 edgecolor
-newpath 665.95 106.66 moveto
-658.24 113.92 lineto
-668.8 113.05 lineto
+newpath 480.43 91.75 moveto
+474.11 100.25 lineto
+484.35 97.55 lineto
closepath fill
1 setlinewidth
solid
0 1 1 edgecolor
-newpath 665.95 106.66 moveto
-658.24 113.92 lineto
-668.8 113.05 lineto
+newpath 480.43 91.75 moveto
+474.11 100.25 lineto
+484.35 97.55 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-676 112.4 moveto 48 (RR: [1]) alignedtext
+492 95.4 moveto 48 (RR: [2]) alignedtext
+grestore
+% CAG->CCA
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 697.95 106.92 moveto
+692.17 104.47 686 102.31 680 101 curveto
+659.15 96.47 652.72 95.92 632 101 curveto
+629.21 101.68 626.4 102.57 623.63 103.6 curveto
+stroke
+0 1 1 edgecolor
+newpath 622.19 100.4 moveto
+614.36 107.54 lineto
+624.93 106.84 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 622.19 100.4 moveto
+614.36 107.54 lineto
+624.93 106.84 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+632 106.4 moveto 48 (RR: [2]) alignedtext
+grestore
+% AGC
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 838 88 moveto
+838 192 lineto
+894 192 lineto
+894 88 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+850.5 175.4 moveto 31 (AGC) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 838 166 moveto
+894 166 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+852 149.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 838 140 moveto
+894 140 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+846 123.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 838 114 moveto
+894 114 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+854.5 97.4 moveto 23 (1.0) alignedtext
+grestore
+% CAG->AGC
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 754.33 125.64 moveto
+775.39 128.35 804.37 132.08 827.53 135.05 curveto
+stroke
+0 0 0 edgecolor
+newpath 827.35 138.56 moveto
+837.71 136.36 lineto
+828.24 131.62 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 827.35 138.56 moveto
+837.71 136.36 lineto
+828.24 131.62 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+773.5 138.4 moveto 45 (FF: [2]) alignedtext
+grestore
+% ACC->CCA
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 474.33 128.99 moveto
+495.39 128.24 524.37 127.2 547.53 126.37 curveto
+stroke
+0 0 0 edgecolor
+newpath 547.84 129.87 moveto
+557.71 126.01 lineto
+547.59 122.87 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 547.84 129.87 moveto
+557.71 126.01 lineto
+547.59 122.87 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+493.5 133.4 moveto 45 (FF: [2]) alignedtext
+grestore
+% ACC->AGG
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 417.82 108.07 moveto
+412.19 104.74 406.12 101.82 400 100 curveto
+380.4 94.17 373.15 92.84 354 100 curveto
+350.73 101.22 347.54 102.8 344.46 104.61 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 342.43 101.75 moveto
+336.11 110.25 lineto
+346.35 107.55 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 342.43 101.75 moveto
+336.11 110.25 lineto
+346.35 107.55 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+354 105.4 moveto 46 (FR: [1]) alignedtext
+grestore
+% ACG->CGA
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 1322.27 121.77 moveto
+1344.16 121.62 1372.89 121.42 1395.74 121.26 curveto
+stroke
+0 0 0 edgecolor
+newpath 1395.8 124.76 moveto
+1405.77 121.19 lineto
+1395.75 117.76 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 1395.8 124.76 moveto
+1405.77 121.19 lineto
+1395.75 117.76 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+1341.5 126.4 moveto 45 (FF: [1]) alignedtext
+grestore
+% CCG
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1118 73 moveto
+1118 177 lineto
+1174 177 lineto
+1174 73 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1130.5 160.4 moveto 31 (CCG) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1118 151 moveto
+1174 151 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1132 134.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1118 125 moveto
+1174 125 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1126 108.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1118 99 moveto
+1174 99 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1134.5 82.4 moveto 23 (1.0) alignedtext
+grestore
+% ACG->CCG
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 1255.78 93.53 moveto
+1250.16 90.03 1244.14 86.99 1238 85 curveto
+1218.55 78.69 1211.15 77.84 1192 85 curveto
+1188.73 86.22 1185.54 87.8 1182.46 89.61 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 1180.43 86.75 moveto
+1174.11 95.25 lineto
+1184.35 92.55 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 1180.43 86.75 moveto
+1174.11 95.25 lineto
+1184.35 92.55 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+1192 90.4 moveto 46 (FR: [2]) alignedtext
+grestore
+% AGG->AAG
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 279.64 122.54 moveto
+273.98 119.84 267.95 117.46 262 116 curveto
+244.12 111.62 223.78 112.06 206.61 113.93 curveto
+stroke
+0 1 1 edgecolor
+newpath 205.84 110.5 moveto
+196.37 115.25 lineto
+206.74 117.44 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 205.84 110.5 moveto
+196.37 115.25 lineto
+206.74 117.44 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+214 121.4 moveto 48 (RR: [1]) alignedtext
+grestore
+% AGG->ACC
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 336.26 137.95 moveto
+356.82 136.46 384.89 134.43 407.5 132.79 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 408.06 136.26 moveto
+417.78 132.05 lineto
+407.55 129.28 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 408.06 136.26 moveto
+417.78 132.05 lineto
+407.55 129.28 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+354 141.4 moveto 46 (FR: [1]) alignedtext
+grestore
+% GCC
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 978 78 moveto
+978 182 lineto
+1034 182 lineto
+1034 78 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+990.5 165.4 moveto 31 (GCC) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 978 156 moveto
+1034 156 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+992 139.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 978 130 moveto
+1034 130 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+986 113.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 978 104 moveto
+1034 104 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+994.5 87.4 moveto 23 (1.0) alignedtext
+grestore
+% GCC->CCG
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 1034.33 128.99 moveto
+1055.39 128.24 1084.37 127.2 1107.53 126.37 curveto
+stroke
+0 0 0 edgecolor
+newpath 1107.84 129.87 moveto
+1117.71 126.01 lineto
+1107.59 122.87 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 1107.84 129.87 moveto
+1117.71 126.01 lineto
+1107.59 122.87 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+1053.5 133.4 moveto 45 (FF: [2]) alignedtext
+grestore
+% GCC->AGC
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 977.82 108.07 moveto
+972.19 104.74 966.12 101.82 960 100 curveto
+939.55 93.92 931.98 92.53 912 100 curveto
+908.73 101.22 905.54 102.8 902.46 104.61 curveto
+stroke
+0 1 1 edgecolor
+newpath 900.43 101.75 moveto
+894.11 110.25 lineto
+904.35 107.55 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 900.43 101.75 moveto
+894.11 110.25 lineto
+904.35 107.55 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+912 105.4 moveto 48 (RR: [2]) alignedtext
+grestore
+% CCG->ACG
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 1174.25 124.41 moveto
+1194.58 123.98 1222.38 123.4 1245.53 122.91 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 1245.86 126.41 moveto
+1255.79 122.7 lineto
+1245.72 119.41 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 1245.86 126.41 moveto
+1255.79 122.7 lineto
+1245.72 119.41 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+1192 129.4 moveto 46 (FR: [2]) alignedtext
+grestore
+% CCG->GCC
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 1117.95 109.92 moveto
+1112.17 107.47 1106 105.31 1100 104 curveto
+1079.15 99.47 1072.63 98.57 1052 104 curveto
+1049.17 104.74 1046.34 105.71 1043.54 106.82 curveto
+stroke
+0 1 1 edgecolor
+newpath 1041.85 103.74 moveto
+1034.23 111.1 lineto
+1044.77 110.1 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 1041.85 103.74 moveto
+1034.23 111.1 lineto
+1044.77 110.1 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+1052 109.4 moveto 48 (RR: [2]) alignedtext
+grestore
+% AGC->CAG
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 837.97 111.91 moveto
+832.42 107.85 826.34 104.28 820 102 curveto
+799.93 94.78 792.89 97.66 772 102 curveto
+769.2 102.58 766.37 103.34 763.55 104.23 curveto
+stroke
+0 1 1 edgecolor
+newpath 762.33 100.95 moveto
+754.11 107.63 lineto
+764.71 107.53 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 762.33 100.95 moveto
+754.11 107.63 lineto
+764.71 107.53 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+772 107.4 moveto 48 (RR: [2]) alignedtext
+grestore
+% AGC->GCC
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 894.33 137.98 moveto
+915.39 136.47 944.37 134.4 967.53 132.75 curveto
+stroke
+0 0 0 edgecolor
+newpath 967.99 136.22 moveto
+977.71 132.02 lineto
+967.49 129.24 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 967.99 136.22 moveto
+977.71 132.02 lineto
+967.49 129.24 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+913.5 141.4 moveto 45 (FF: [2]) alignedtext
grestore
endpage
showpage
@@ -913,7 +1223,7 @@
%%EndPage: 1
%%Trailer
%%Pages: 1
-%%BoundingBox: 36 36 1122 232
+%%BoundingBox: 36 36 1646 236
end
restore
%%EOF
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoL/..binmerge.crc b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoL/..binmerge.crc
index a266402..07ad328 100644
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoL/..binmerge.crc
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoL/..binmerge.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoL/.binmerge b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoL/.binmerge
index 60a2335..d6b6cf4 100755
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoL/.binmerge
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoL/.binmerge
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoL/bin/.part-00000.crc b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoL/bin/.part-00000.crc
index 2b529fb..7bf3d09 100644
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoL/bin/.part-00000.crc
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoL/bin/.part-00000.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoL/bin/part-00000 b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoL/bin/part-00000
index 2908263..34ece44 100755
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoL/bin/part-00000
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoL/bin/part-00000
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoL/data b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoL/data
index 36b42d0..be08224 100644
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoL/data
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoL/data
@@ -1,8 +1,12 @@
-AAA {[] [] [] [{GAA:[6]}, {CAA:[5]}] {5':[], ~5':[]} 2.0x}
-CAA {[{AAA:[5]}] [] [] [{ACA:[3]}] {5':[(5-0_0)], ~5':[]} 2.0x}
-GAA {[{AAA:[6]}] [] [] [{AGA:[4]}] {5':[(6-0_0)], ~5':[(4-0_0)]} 2.0x}
-TAA {[{AAG:[2]}, {AAC:[1]}] [] [] [] {5':[], ~5':[]} 2.0x}
-ACA {[{CAA:[3]}] [] [] [{AAC:[3]}] {5':[], ~5':[]} 1.0x}
-AGA {[{GAA:[4]}] [] [] [{AAG:[4]}] {5':[], ~5':[]} 1.0x}
-AAC {[{ACA:[3]}] [] [] [{TAA:[1]}] {5':[(3-0_0)], ~5':[(1-0_0)]} 2.0x}
-AAG {[{AGA:[4]}] [] [] [{TAA:[2]}] {5':[], ~5':[(2-0_0)]} 2.0x}
+AAA {[{AAG:[1]}] [] [] [{GAA:[1]}] {5':[], ~5':[]} 1.0x}
+GAA {[{AAA:[1]}] [] [] [{CGA:[1]}] {5':[], ~5':[]} 1.0x}
+CCA {[{CAG:[2]}] [] [{GGA:[2]}] [] {5':[], ~5':[]} 1.0x}
+CGA {[{GAA:[1]}] [] [{CGC:[1]}] [] {5':[], ~5':[]} 1.0x}
+GGA {[] [] [{CCA:[2]}] [{AGG:[1]}] {5':[], ~5':[]} 2.0x}
+GCC {[{CCG:[2]}] [] [] [{AGC:[2]}] {5':[], ~5':[]} 1.0x}
+AGC {[{GCC:[2]}] [] [] [{CAG:[2]}] {5':[], ~5':[]} 1.0x}
+CGC {[] [] [{CGA:[1]}] [{CCG:[2]}] {5':[], ~5':[(2-0_0),(1-0_0)]} 2.0x}
+AAG {[{AGG:[1]}] [] [] [{AAA:[1]}] {5':[], ~5':[]} 1.0x}
+CAG {[{AGC:[2]}] [] [] [{CCA:[2]}] {5':[], ~5':[]} 1.0x}
+CCG {[{CGC:[2]}] [] [] [{GCC:[2]}] {5':[], ~5':[]} 1.0x}
+AGG {[{GGA:[1]}] [] [] [{AAG:[1]}] {5':[], ~5':[]} 1.0x}
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoL/graphviz/result.ps b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoL/graphviz/result.ps
index 1df55ef..aac6f8b 100644
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoL/graphviz/result.ps
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoL/graphviz/result.ps
@@ -178,11 +178,11 @@
%%EndSetup
setupLatin1
%%Page: 1 1
-%%PageBoundingBox: 36 36 1110 232
+%%PageBoundingBox: 36 36 1658 236
%%PageOrientation: Portrait
0 0 1 beginpage
gsave
-36 36 1074 196 boxprim clip newpath
+36 36 1622 200 boxprim clip newpath
1 1 set_scale 0 rotate 40 41 translate
% AAA
gsave
@@ -219,691 +219,1002 @@
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-16.5 15.4 moveto 23 (2.0) alignedtext
+16.5 15.4 moveto 23 (1.0) alignedtext
grestore
-% GAA
+% AAG
gsave
-0 0 0.75294 nodecolor
-newpath 140.5 69 moveto
-140.5 173 lineto
-205.5 173 lineto
-205.5 69 lineto
-closepath fill
1 setlinewidth
-filled
0 0 0 nodecolor
-newpath 140.5 69 moveto
-140.5 173 lineto
-205.5 173 lineto
-205.5 69 lineto
+newpath 140 69 moveto
+140 173 lineto
+196 173 lineto
+196 69 lineto
closepath stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-157 156.4 moveto 32 (GAA) alignedtext
+152 156.4 moveto 32 (AAG) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
-newpath 140.5 147 moveto
-205.5 147 lineto
+newpath 140 147 moveto
+196 147 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-154.5 130.4 moveto 37 (5':[6]) alignedtext
+154 130.4 moveto 28 (5':[]) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
-newpath 140.5 121 moveto
-205.5 121 lineto
+newpath 140 121 moveto
+196 121 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-148.5 104.4 moveto 49 (~5':[4]) alignedtext
+148 104.4 moveto 40 (~5':[]) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
-newpath 140.5 95 moveto
-205.5 95 lineto
+newpath 140 95 moveto
+196 95 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-161.5 78.4 moveto 23 (2.0) alignedtext
+156.5 78.4 moveto 23 (1.0) alignedtext
+grestore
+% AAA->AAG
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 56 85.12 moveto
+61.65 89.58 67.77 93.78 74 97 curveto
+91.26 105.91 112.06 111.67 129.69 115.3 curveto
+stroke
+0 0 0 edgecolor
+newpath 129.18 118.76 moveto
+139.66 117.2 lineto
+130.49 111.89 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 129.18 118.76 moveto
+139.66 117.2 lineto
+130.49 111.89 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+75.5 118.4 moveto 45 (FF: [1]) alignedtext
+grestore
+% GAA
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1558 7 moveto
+1558 111 lineto
+1614 111 lineto
+1614 7 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1570 94.4 moveto 32 (GAA) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1558 85 moveto
+1614 85 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1572 68.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1558 59 moveto
+1614 59 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1566 42.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1558 33 moveto
+1614 33 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1574.5 16.4 moveto 23 (1.0) alignedtext
grestore
% AAA->GAA
gsave
1 setlinewidth
0 1 1 edgecolor
-newpath 56.23 85.38 moveto
-61.8 89.76 67.84 93.87 74 97 curveto
-91.48 105.89 112.38 111.58 130.47 115.18 curveto
+newpath 56.03 52.57 moveto
+84.21 47.6 128.95 41 168 41 curveto
+168 41 168 41 1446 41 curveto
+1480.66 41 1519.75 46.49 1547.8 51.41 curveto
stroke
0 1 1 edgecolor
-newpath 130 118.65 moveto
-140.47 117.01 lineto
-131.26 111.76 lineto
+newpath 1547.52 54.92 moveto
+1557.98 53.26 lineto
+1548.76 48.03 lineto
closepath fill
1 setlinewidth
solid
0 1 1 edgecolor
-newpath 130 118.65 moveto
-140.47 117.01 lineto
-131.26 111.76 lineto
+newpath 1547.52 54.92 moveto
+1557.98 53.26 lineto
+1548.76 48.03 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-74 118.4 moveto 48 (RR: [6]) alignedtext
+772 46.4 moveto 48 (RR: [1]) alignedtext
grestore
-% CAA
-gsave
-0 0 0.75294 nodecolor
-newpath 1010 7 moveto
-1010 111 lineto
-1066 111 lineto
-1066 7 lineto
-closepath fill
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 1010 7 moveto
-1010 111 lineto
-1066 111 lineto
-1066 7 lineto
-closepath stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-1022.5 94.4 moveto 31 (CAA) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 1010 85 moveto
-1066 85 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-1019.5 68.4 moveto 37 (5':[5]) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 1010 59 moveto
-1066 59 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-1018 42.4 moveto 40 (~5':[]) alignedtext
-1 setlinewidth
-filled
-0 0 0 nodecolor
-newpath 1010 33 moveto
-1066 33 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-1026.5 16.4 moveto 23 (2.0) alignedtext
-grestore
-% AAA->CAA
+% AAG->AAA
gsave
1 setlinewidth
0 1 1 edgecolor
-newpath 56.23 52.71 moveto
-85.36 47.72 132.19 41 173 41 curveto
-173 41 173 41 898 41 curveto
-932.66 41 971.75 46.49 999.8 51.41 curveto
+newpath 139.99 87.84 moveto
+134.48 82.9 128.4 78.35 122 75 curveto
+104.93 66.06 83.99 61.74 66.21 59.68 curveto
stroke
0 1 1 edgecolor
-newpath 999.52 54.92 moveto
-1009.98 53.26 lineto
-1000.76 48.03 lineto
+newpath 66.45 56.18 moveto
+56.16 58.71 lineto
+65.78 63.15 lineto
closepath fill
1 setlinewidth
solid
0 1 1 edgecolor
-newpath 999.52 54.92 moveto
-1009.98 53.26 lineto
-1000.76 48.03 lineto
+newpath 66.45 56.18 moveto
+56.16 58.71 lineto
+65.78 63.15 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-514 46.4 moveto 48 (RR: [5]) alignedtext
+74 80.4 moveto 48 (RR: [1]) alignedtext
+grestore
+% AGG
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 280 88 moveto
+280 192 lineto
+336 192 lineto
+336 88 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+291.5 175.4 moveto 33 (AGG) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 280 166 moveto
+336 166 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+294 149.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 280 140 moveto
+336 140 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+288 123.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 280 114 moveto
+336 114 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+296.5 97.4 moveto 23 (1.0) alignedtext
+grestore
+% AAG->AGG
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 196.29 133.12 moveto
+202.05 135.11 208.14 136.89 214 138 curveto
+232.06 141.43 252.42 142.23 269.57 142.05 curveto
+stroke
+0 0 0 edgecolor
+newpath 269.86 145.54 moveto
+279.78 141.82 lineto
+269.7 138.54 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 269.86 145.54 moveto
+279.78 141.82 lineto
+269.7 138.54 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+215.5 147.4 moveto 45 (FF: [1]) alignedtext
grestore
% GAA->AAA
gsave
1 setlinewidth
0 0 0 edgecolor
-newpath 140.38 86.94 moveto
-134.64 82.35 128.42 78.15 122 75 curveto
-104.83 66.57 84.04 62.28 66.39 60.12 curveto
+newpath 1557.96 39.35 moveto
+1530.68 22.19 1487.41 0 1446 0 curveto
+168 0 168 0 168 0 curveto
+130.89 0 92.17 17.61 64.88 33.42 curveto
stroke
0 0 0 edgecolor
-newpath 66.72 56.64 moveto
-56.41 59.08 lineto
-65.99 63.6 lineto
+newpath 62.87 30.55 moveto
+56.09 38.69 lineto
+66.46 36.55 lineto
closepath fill
1 setlinewidth
solid
0 0 0 edgecolor
-newpath 66.72 56.64 moveto
-56.41 59.08 lineto
-65.99 63.6 lineto
+newpath 62.87 30.55 moveto
+56.09 38.69 lineto
+66.46 36.55 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-75.5 80.4 moveto 45 (FF: [6]) alignedtext
+773.5 5.4 moveto 45 (FF: [1]) alignedtext
grestore
-% AGA
+% CGA
gsave
1 setlinewidth
0 0 0 nodecolor
-newpath 290 80 moveto
-290 184 lineto
-346 184 lineto
-346 80 lineto
+newpath 1418 69 moveto
+1418 173 lineto
+1474 173 lineto
+1474 69 lineto
closepath stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-302.5 167.4 moveto 31 (AGA) alignedtext
+1430.5 156.4 moveto 31 (CGA) alignedtext
1 setlinewidth
0 0 0 nodecolor
-newpath 290 158 moveto
-346 158 lineto
+newpath 1418 147 moveto
+1474 147 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-304 141.4 moveto 28 (5':[]) alignedtext
+1432 130.4 moveto 28 (5':[]) alignedtext
1 setlinewidth
0 0 0 nodecolor
-newpath 290 132 moveto
-346 132 lineto
+newpath 1418 121 moveto
+1474 121 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-298 115.4 moveto 40 (~5':[]) alignedtext
+1426 104.4 moveto 40 (~5':[]) alignedtext
1 setlinewidth
0 0 0 nodecolor
-newpath 290 106 moveto
-346 106 lineto
+newpath 1418 95 moveto
+1474 95 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-306.5 89.4 moveto 23 (1.0) alignedtext
+1434.5 78.4 moveto 23 (1.0) alignedtext
grestore
-% GAA->AGA
+% GAA->CGA
gsave
1 setlinewidth
0 1 1 edgecolor
-newpath 205.55 127.51 moveto
-211.65 128.51 218 129.41 224 130 curveto
-242.3 131.8 262.69 132.4 279.79 132.51 curveto
+newpath 1557.97 61.07 moveto
+1538.57 63.41 1512.63 68.4 1492 79 curveto
+1488.68 80.71 1485.42 82.72 1482.26 84.92 curveto
stroke
0 1 1 edgecolor
-newpath 279.96 136.01 moveto
-289.96 132.53 lineto
-279.97 129.01 lineto
+newpath 1479.98 82.26 moveto
+1474.17 91.11 lineto
+1484.24 87.81 lineto
closepath fill
1 setlinewidth
solid
0 1 1 edgecolor
-newpath 279.96 136.01 moveto
-289.96 132.53 lineto
-279.97 129.01 lineto
+newpath 1479.98 82.26 moveto
+1474.17 91.11 lineto
+1484.24 87.81 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-224 137.4 moveto 48 (RR: [4]) alignedtext
+1492 84.4 moveto 48 (RR: [1]) alignedtext
grestore
-% CAA->AAA
+% CGA->GAA
gsave
1 setlinewidth
0 0 0 edgecolor
-newpath 1009.96 39.35 moveto
-982.68 22.19 939.41 0 898 0 curveto
-173 0 173 0 173 0 curveto
-134.1 0 93.26 18.22 64.87 34.23 curveto
+newpath 1474.3 117.12 moveto
+1493.58 113.68 1519.28 107.53 1540 97 curveto
+1543.29 95.33 1546.55 93.39 1549.73 91.29 curveto
stroke
0 0 0 edgecolor
-newpath 62.99 31.28 moveto
-56.11 39.33 lineto
-66.51 37.33 lineto
+newpath 1551.83 94.08 moveto
+1557.92 85.41 lineto
+1547.75 88.4 lineto
closepath fill
1 setlinewidth
solid
0 0 0 edgecolor
-newpath 62.99 31.28 moveto
-56.11 39.33 lineto
-66.51 37.33 lineto
+newpath 1551.83 94.08 moveto
+1557.92 85.41 lineto
+1547.75 88.4 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-515.5 5.4 moveto 45 (FF: [5]) alignedtext
+1493.5 118.4 moveto 45 (FF: [1]) alignedtext
grestore
-% ACA
-gsave
-1 setlinewidth
-0 0 0 nodecolor
-newpath 870 69 moveto
-870 173 lineto
-926 173 lineto
-926 69 lineto
-closepath stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-883 156.4 moveto 30 (ACA) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 870 147 moveto
-926 147 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-884 130.4 moveto 28 (5':[]) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 870 121 moveto
-926 121 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-878 104.4 moveto 40 (~5':[]) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 870 95 moveto
-926 95 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-886.5 78.4 moveto 23 (1.0) alignedtext
-grestore
-% CAA->ACA
-gsave
-1 setlinewidth
-0 1 1 edgecolor
-newpath 1009.97 61.07 moveto
-990.57 63.41 964.63 68.4 944 79 curveto
-940.68 80.71 937.42 82.72 934.26 84.92 curveto
-stroke
-0 1 1 edgecolor
-newpath 931.98 82.26 moveto
-926.17 91.11 lineto
-936.24 87.81 lineto
-closepath fill
-1 setlinewidth
-solid
-0 1 1 edgecolor
-newpath 931.98 82.26 moveto
-926.17 91.11 lineto
-936.24 87.81 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-944 84.4 moveto 48 (RR: [3]) alignedtext
-grestore
-% ACA->CAA
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 926.3 117.12 moveto
-945.58 113.68 971.28 107.53 992 97 curveto
-995.29 95.33 998.55 93.39 1001.73 91.29 curveto
-stroke
-0 0 0 edgecolor
-newpath 1003.83 94.08 moveto
-1009.92 85.41 lineto
-999.75 88.4 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 1003.83 94.08 moveto
-1009.92 85.41 lineto
-999.75 88.4 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-945.5 118.4 moveto 45 (FF: [3]) alignedtext
-grestore
-% AAC
+% CGC
gsave
0 0 0.75294 nodecolor
-newpath 720.5 74 moveto
-720.5 178 lineto
-785.5 178 lineto
-785.5 74 lineto
+newpath 1258 70 moveto
+1258 174 lineto
+1336 174 lineto
+1336 70 lineto
closepath fill
1 setlinewidth
filled
0 0 0 nodecolor
-newpath 720.5 74 moveto
-720.5 178 lineto
-785.5 178 lineto
-785.5 74 lineto
+newpath 1258 70 moveto
+1258 174 lineto
+1336 174 lineto
+1336 70 lineto
closepath stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-737.5 161.4 moveto 31 (AAC) alignedtext
+1281.5 157.4 moveto 31 (CGC) alignedtext
1 setlinewidth
filled
0 0 0 nodecolor
-newpath 720.5 152 moveto
-785.5 152 lineto
+newpath 1258 148 moveto
+1336 148 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-734.5 135.4 moveto 37 (5':[3]) alignedtext
+1283 131.4 moveto 28 (5':[]) alignedtext
1 setlinewidth
filled
0 0 0 nodecolor
-newpath 720.5 126 moveto
-785.5 126 lineto
+newpath 1258 122 moveto
+1336 122 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-728.5 109.4 moveto 49 (~5':[1]) alignedtext
+1266 105.4 moveto 62 (~5':[2,1]) alignedtext
1 setlinewidth
filled
0 0 0 nodecolor
-newpath 720.5 100 moveto
-785.5 100 lineto
+newpath 1258 96 moveto
+1336 96 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-741.5 83.4 moveto 23 (2.0) alignedtext
+1285.5 79.4 moveto 23 (2.0) alignedtext
grestore
-% ACA->AAC
+% CGA->CGC
gsave
1 setlinewidth
-0 1 1 edgecolor
-newpath 869.97 95.28 moveto
-864.37 91.47 858.28 88.12 852 86 curveto
-831.78 79.18 824.16 79.04 804 86 curveto
-800.71 87.14 797.47 88.58 794.32 90.25 curveto
+0.33333 1 1 edgecolor
+newpath 1417.8 91.99 moveto
+1412.31 87.9 1406.29 84.31 1400 82 curveto
+1380.81 74.96 1373.5 75.84 1354 82 curveto
+1351.04 82.93 1348.1 84.08 1345.21 85.4 curveto
stroke
-0 1 1 edgecolor
-newpath 792.45 87.28 moveto
-785.69 95.44 lineto
-796.06 93.28 lineto
+0.33333 1 1 edgecolor
+newpath 1343.43 82.37 moveto
+1336.16 90.07 lineto
+1346.65 88.59 lineto
closepath fill
1 setlinewidth
solid
-0 1 1 edgecolor
-newpath 792.45 87.28 moveto
-785.69 95.44 lineto
-796.06 93.28 lineto
+0.33333 1 1 edgecolor
+newpath 1343.43 82.37 moveto
+1336.16 90.07 lineto
+1346.65 88.59 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-804 91.4 moveto 48 (RR: [3]) alignedtext
+1354 87.4 moveto 46 (RF: [1]) alignedtext
grestore
-% AGA->GAA
+% CCA
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 558 73 moveto
+558 177 lineto
+614 177 lineto
+614 73 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+571 160.4 moveto 30 (CCA) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 558 151 moveto
+614 151 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+572 134.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 558 125 moveto
+614 125 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+566 108.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 558 99 moveto
+614 99 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+574.5 82.4 moveto 23 (1.0) alignedtext
+grestore
+% CAG
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 698 70 moveto
+698 174 lineto
+754 174 lineto
+754 70 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+710.5 157.4 moveto 31 (CAG) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 698 148 moveto
+754 148 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+712 131.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 698 122 moveto
+754 122 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+706 105.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 698 96 moveto
+754 96 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+714.5 79.4 moveto 23 (1.0) alignedtext
+grestore
+% CCA->CAG
gsave
1 setlinewidth
0 0 0 edgecolor
-newpath 289.64 114.54 moveto
-283.98 111.84 277.95 109.46 272 108 curveto
-253.84 103.55 233.42 105.15 215.86 108.5 curveto
+newpath 614.33 124.39 moveto
+635.39 123.94 664.37 123.32 687.53 122.82 curveto
stroke
0 0 0 edgecolor
-newpath 214.93 105.12 moveto
-205.88 110.64 lineto
-216.4 111.97 lineto
+newpath 687.79 126.32 moveto
+697.71 122.61 lineto
+687.64 119.32 lineto
closepath fill
1 setlinewidth
solid
0 0 0 edgecolor
-newpath 214.93 105.12 moveto
-205.88 110.64 lineto
-216.4 111.97 lineto
+newpath 687.79 126.32 moveto
+697.71 122.61 lineto
+687.64 119.32 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-225.5 113.4 moveto 45 (FF: [4]) alignedtext
+633.5 128.4 moveto 45 (FF: [2]) alignedtext
grestore
-% AAG
+% GGA
gsave
-0 0 0.75294 nodecolor
-newpath 430.5 70 moveto
-430.5 174 lineto
-495.5 174 lineto
-495.5 70 lineto
-closepath fill
1 setlinewidth
-filled
0 0 0 nodecolor
-newpath 430.5 70 moveto
-430.5 174 lineto
-495.5 174 lineto
-495.5 70 lineto
+newpath 420 78 moveto
+420 182 lineto
+476 182 lineto
+476 78 lineto
closepath stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-447 157.4 moveto 32 (AAG) alignedtext
+431.5 165.4 moveto 33 (GGA) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
-newpath 430.5 148 moveto
-495.5 148 lineto
+newpath 420 156 moveto
+476 156 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-449 131.4 moveto 28 (5':[]) alignedtext
+434 139.4 moveto 28 (5':[]) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
-newpath 430.5 122 moveto
-495.5 122 lineto
+newpath 420 130 moveto
+476 130 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-438.5 105.4 moveto 49 (~5':[2]) alignedtext
+428 113.4 moveto 40 (~5':[]) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
-newpath 430.5 96 moveto
-495.5 96 lineto
+newpath 420 104 moveto
+476 104 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-451.5 79.4 moveto 23 (2.0) alignedtext
+436.5 87.4 moveto 23 (2.0) alignedtext
grestore
-% AGA->AAG
+% CCA->GGA
+gsave
+1 setlinewidth
+0.33333 1 1 edgecolor
+newpath 557.97 99.28 moveto
+552.37 95.47 546.28 92.12 540 90 curveto
+520.63 83.47 513.15 82.84 494 90 curveto
+490.73 91.22 487.54 92.8 484.46 94.61 curveto
+stroke
+0.33333 1 1 edgecolor
+newpath 482.43 91.75 moveto
+476.11 100.25 lineto
+486.35 97.55 lineto
+closepath fill
+1 setlinewidth
+solid
+0.33333 1 1 edgecolor
+newpath 482.43 91.75 moveto
+476.11 100.25 lineto
+486.35 97.55 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+494 95.4 moveto 46 (RF: [2]) alignedtext
+grestore
+% CAG->CCA
gsave
1 setlinewidth
0 1 1 edgecolor
-newpath 346.3 130.05 moveto
-367.34 128.6 396.4 126.59 420.26 124.95 curveto
+newpath 697.95 106.92 moveto
+692.17 104.47 686 102.31 680 101 curveto
+659.15 96.47 652.72 95.92 632 101 curveto
+629.21 101.68 626.4 102.57 623.63 103.6 curveto
stroke
0 1 1 edgecolor
-newpath 420.73 128.42 moveto
-430.47 124.24 lineto
-420.25 121.44 lineto
+newpath 622.19 100.4 moveto
+614.36 107.54 lineto
+624.93 106.84 lineto
closepath fill
1 setlinewidth
solid
0 1 1 edgecolor
-newpath 420.73 128.42 moveto
-430.47 124.24 lineto
-420.25 121.44 lineto
+newpath 622.19 100.4 moveto
+614.36 107.54 lineto
+624.93 106.84 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-364 133.4 moveto 48 (RR: [4]) alignedtext
+632 106.4 moveto 48 (RR: [2]) alignedtext
grestore
-% TAA
+% AGC
gsave
1 setlinewidth
0 0 0 nodecolor
-newpath 580 84 moveto
-580 188 lineto
-636 188 lineto
-636 84 lineto
+newpath 838 88 moveto
+838 192 lineto
+894 192 lineto
+894 88 lineto
closepath stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-593.5 171.4 moveto 29 (TAA) alignedtext
+850.5 175.4 moveto 31 (AGC) alignedtext
1 setlinewidth
0 0 0 nodecolor
-newpath 580 162 moveto
-636 162 lineto
+newpath 838 166 moveto
+894 166 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-594 145.4 moveto 28 (5':[]) alignedtext
+852 149.4 moveto 28 (5':[]) alignedtext
1 setlinewidth
0 0 0 nodecolor
-newpath 580 136 moveto
-636 136 lineto
+newpath 838 140 moveto
+894 140 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-588 119.4 moveto 40 (~5':[]) alignedtext
+846 123.4 moveto 40 (~5':[]) alignedtext
1 setlinewidth
0 0 0 nodecolor
-newpath 580 110 moveto
-636 110 lineto
+newpath 838 114 moveto
+894 114 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-596.5 93.4 moveto 23 (2.0) alignedtext
+854.5 97.4 moveto 23 (1.0) alignedtext
grestore
-% TAA->AAG
+% CAG->AGC
gsave
1 setlinewidth
0 0 0 edgecolor
-newpath 579.88 111 moveto
-574.3 107.3 568.23 104.05 562 102 curveto
-543.73 95.98 522.94 98.79 505.15 103.97 curveto
+newpath 754.33 125.64 moveto
+775.39 128.35 804.37 132.08 827.53 135.05 curveto
stroke
0 0 0 edgecolor
-newpath 504.05 100.65 moveto
-495.61 107.05 lineto
-506.2 107.31 lineto
+newpath 827.35 138.56 moveto
+837.71 136.36 lineto
+828.24 131.62 lineto
closepath fill
1 setlinewidth
solid
0 0 0 edgecolor
-newpath 504.05 100.65 moveto
-495.61 107.05 lineto
-506.2 107.31 lineto
+newpath 827.35 138.56 moveto
+837.71 136.36 lineto
+828.24 131.62 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-515.5 107.4 moveto 45 (FF: [2]) alignedtext
+773.5 138.4 moveto 45 (FF: [2]) alignedtext
grestore
-% TAA->AAC
+% GGA->CCA
gsave
1 setlinewidth
-0 0 0 edgecolor
-newpath 636.3 134.05 moveto
-657.34 132.6 686.4 130.59 710.26 128.95 curveto
+0.33333 1 1 edgecolor
+newpath 476.26 128.98 moveto
+496.82 128.23 524.89 127.21 547.5 126.39 curveto
stroke
-0 0 0 edgecolor
-newpath 710.73 132.42 moveto
-720.47 128.24 lineto
-710.25 125.44 lineto
+0.33333 1 1 edgecolor
+newpath 547.91 129.88 moveto
+557.78 126.02 lineto
+547.66 122.89 lineto
closepath fill
1 setlinewidth
solid
-0 0 0 edgecolor
-newpath 710.73 132.42 moveto
-720.47 128.24 lineto
-710.25 125.44 lineto
+0.33333 1 1 edgecolor
+newpath 547.91 129.88 moveto
+557.78 126.02 lineto
+547.66 122.89 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-655.5 137.4 moveto 45 (FF: [1]) alignedtext
+494 133.4 moveto 46 (RF: [2]) alignedtext
grestore
-% AAG->AGA
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 430.29 107.87 moveto
-424.31 105.85 418.04 104.09 412 103 curveto
-391 99.22 384.5 97.08 364 103 curveto
-361.01 103.86 358.03 104.98 355.11 106.28 curveto
-stroke
-0 0 0 edgecolor
-newpath 353.32 103.27 moveto
-346.01 110.93 lineto
-356.51 109.5 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 353.32 103.27 moveto
-346.01 110.93 lineto
-356.51 109.5 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-365.5 108.4 moveto 45 (FF: [4]) alignedtext
-grestore
-% AAG->TAA
+% GGA->AGG
gsave
1 setlinewidth
0 1 1 edgecolor
-newpath 495.54 125.14 moveto
-517.55 127.27 546.71 130.08 569.82 132.31 curveto
+newpath 419.82 108.07 moveto
+414.19 104.74 408.12 101.82 402 100 curveto
+381.55 93.92 373.98 92.53 354 100 curveto
+350.73 101.22 347.54 102.8 344.46 104.61 curveto
stroke
0 1 1 edgecolor
-newpath 569.68 135.82 moveto
-579.97 133.29 lineto
-570.35 128.85 lineto
+newpath 342.43 101.75 moveto
+336.11 110.25 lineto
+346.35 107.55 lineto
closepath fill
1 setlinewidth
solid
0 1 1 edgecolor
-newpath 569.68 135.82 moveto
-579.97 133.29 lineto
-570.35 128.85 lineto
+newpath 342.43 101.75 moveto
+336.11 110.25 lineto
+346.35 107.55 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-514 136.4 moveto 48 (RR: [2]) alignedtext
+354 105.4 moveto 48 (RR: [1]) alignedtext
grestore
-% AAC->ACA
+% CGC->CGA
gsave
1 setlinewidth
-0 0 0 edgecolor
-newpath 785.54 124.88 moveto
-807.55 124.12 836.71 123.11 859.82 122.32 curveto
+0.33333 1 1 edgecolor
+newpath 1336.15 121.74 moveto
+1358.23 121.59 1385.7 121.4 1407.65 121.26 curveto
stroke
-0 0 0 edgecolor
-newpath 860.09 125.81 moveto
-869.97 121.97 lineto
-859.85 118.81 lineto
+0.33333 1 1 edgecolor
+newpath 1407.96 124.76 moveto
+1417.94 121.19 lineto
+1407.91 117.76 lineto
closepath fill
1 setlinewidth
solid
-0 0 0 edgecolor
-newpath 860.09 125.81 moveto
-869.97 121.97 lineto
-859.85 118.81 lineto
+0.33333 1 1 edgecolor
+newpath 1407.96 124.76 moveto
+1417.94 121.19 lineto
+1407.91 117.76 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-805.5 129.4 moveto 45 (FF: [3]) alignedtext
+1354 126.4 moveto 46 (RF: [1]) alignedtext
grestore
-% AAC->TAA
+% CCG
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1118 73 moveto
+1118 177 lineto
+1174 177 lineto
+1174 73 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1130.5 160.4 moveto 31 (CCG) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1118 151 moveto
+1174 151 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1132 134.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1118 125 moveto
+1174 125 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1126 108.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1118 99 moveto
+1174 99 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1134.5 82.4 moveto 23 (1.0) alignedtext
+grestore
+% CGC->CCG
gsave
1 setlinewidth
0 1 1 edgecolor
-newpath 720.29 111.87 moveto
-714.31 109.85 708.04 108.09 702 107 curveto
-681 103.22 674.5 101.08 654 107 curveto
-651.01 107.86 648.03 108.98 645.11 110.28 curveto
+newpath 1257.95 92.62 moveto
+1252.18 89.5 1246.11 86.81 1240 85 curveto
+1219.54 78.94 1211.98 77.53 1192 85 curveto
+1188.73 86.22 1185.54 87.8 1182.46 89.61 curveto
stroke
0 1 1 edgecolor
-newpath 643.32 107.27 moveto
-636.01 114.93 lineto
-646.51 113.5 lineto
+newpath 1180.43 86.75 moveto
+1174.11 95.25 lineto
+1184.35 92.55 lineto
closepath fill
1 setlinewidth
solid
0 1 1 edgecolor
-newpath 643.32 107.27 moveto
-636.01 114.93 lineto
-646.51 113.5 lineto
+newpath 1180.43 86.75 moveto
+1174.11 95.25 lineto
+1184.35 92.55 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-654 112.4 moveto 48 (RR: [1]) alignedtext
+1192 90.4 moveto 48 (RR: [2]) alignedtext
+grestore
+% AGG->AAG
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 279.64 122.54 moveto
+273.98 119.84 267.95 117.46 262 116 curveto
+244.12 111.62 223.78 112.06 206.61 113.93 curveto
+stroke
+0 1 1 edgecolor
+newpath 205.84 110.5 moveto
+196.37 115.25 lineto
+206.74 117.44 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 205.84 110.5 moveto
+196.37 115.25 lineto
+206.74 117.44 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+214 121.4 moveto 48 (RR: [1]) alignedtext
+grestore
+% AGG->GGA
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 336.33 137.98 moveto
+357.39 136.47 386.37 134.4 409.53 132.75 curveto
+stroke
+0 0 0 edgecolor
+newpath 409.99 136.22 moveto
+419.71 132.02 lineto
+409.49 129.24 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 409.99 136.22 moveto
+419.71 132.02 lineto
+409.49 129.24 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+355.5 141.4 moveto 45 (FF: [1]) alignedtext
+grestore
+% GCC
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 978 78 moveto
+978 182 lineto
+1034 182 lineto
+1034 78 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+990.5 165.4 moveto 31 (GCC) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 978 156 moveto
+1034 156 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+992 139.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 978 130 moveto
+1034 130 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+986 113.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 978 104 moveto
+1034 104 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+994.5 87.4 moveto 23 (1.0) alignedtext
+grestore
+% GCC->CCG
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 1034.33 128.99 moveto
+1055.39 128.24 1084.37 127.2 1107.53 126.37 curveto
+stroke
+0 0 0 edgecolor
+newpath 1107.84 129.87 moveto
+1117.71 126.01 lineto
+1107.59 122.87 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 1107.84 129.87 moveto
+1117.71 126.01 lineto
+1107.59 122.87 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+1053.5 133.4 moveto 45 (FF: [2]) alignedtext
+grestore
+% GCC->AGC
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 977.82 108.07 moveto
+972.19 104.74 966.12 101.82 960 100 curveto
+939.55 93.92 931.98 92.53 912 100 curveto
+908.73 101.22 905.54 102.8 902.46 104.61 curveto
+stroke
+0 1 1 edgecolor
+newpath 900.43 101.75 moveto
+894.11 110.25 lineto
+904.35 107.55 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 900.43 101.75 moveto
+894.11 110.25 lineto
+904.35 107.55 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+912 105.4 moveto 48 (RR: [2]) alignedtext
+grestore
+% CCG->CGC
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 1174.05 124.44 moveto
+1194.65 124.03 1223.17 123.47 1247.55 122.98 curveto
+stroke
+0 0 0 edgecolor
+newpath 1247.79 126.48 moveto
+1257.72 122.78 lineto
+1247.65 119.48 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 1247.79 126.48 moveto
+1257.72 122.78 lineto
+1247.65 119.48 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+1193.5 129.4 moveto 45 (FF: [2]) alignedtext
+grestore
+% CCG->GCC
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 1117.95 109.92 moveto
+1112.17 107.47 1106 105.31 1100 104 curveto
+1079.15 99.47 1072.63 98.57 1052 104 curveto
+1049.17 104.74 1046.34 105.71 1043.54 106.82 curveto
+stroke
+0 1 1 edgecolor
+newpath 1041.85 103.74 moveto
+1034.23 111.1 lineto
+1044.77 110.1 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 1041.85 103.74 moveto
+1034.23 111.1 lineto
+1044.77 110.1 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+1052 109.4 moveto 48 (RR: [2]) alignedtext
+grestore
+% AGC->CAG
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 837.97 111.91 moveto
+832.42 107.85 826.34 104.28 820 102 curveto
+799.93 94.78 792.89 97.66 772 102 curveto
+769.2 102.58 766.37 103.34 763.55 104.23 curveto
+stroke
+0 1 1 edgecolor
+newpath 762.33 100.95 moveto
+754.11 107.63 lineto
+764.71 107.53 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 762.33 100.95 moveto
+754.11 107.63 lineto
+764.71 107.53 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+772 107.4 moveto 48 (RR: [2]) alignedtext
+grestore
+% AGC->GCC
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 894.33 137.98 moveto
+915.39 136.47 944.37 134.4 967.53 132.75 curveto
+stroke
+0 0 0 edgecolor
+newpath 967.99 136.22 moveto
+977.71 132.02 lineto
+967.49 129.24 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 967.99 136.22 moveto
+977.71 132.02 lineto
+967.49 129.24 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+913.5 141.4 moveto 45 (FF: [2]) alignedtext
grestore
endpage
showpage
@@ -912,7 +1223,7 @@
%%EndPage: 1
%%Trailer
%%Pages: 1
-%%BoundingBox: 36 36 1110 232
+%%BoundingBox: 36 36 1658 236
end
restore
%%EOF
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoR/..binmerge.crc b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoR/..binmerge.crc
index 74972ad..717beaa 100644
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoR/..binmerge.crc
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoR/..binmerge.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoR/.binmerge b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoR/.binmerge
index 5a4f976..6606e48 100755
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoR/.binmerge
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoR/.binmerge
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoR/bin/.part-00000.crc b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoR/bin/.part-00000.crc
index 307f1e4..c4154e3 100644
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoR/bin/.part-00000.crc
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoR/bin/.part-00000.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoR/bin/part-00000 b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoR/bin/part-00000
index 479bfb8..eef70bd 100755
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoR/bin/part-00000
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoR/bin/part-00000
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoR/data b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoR/data
index c73b057..0fd492d 100644
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoR/data
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoR/data
@@ -1,8 +1,12 @@
-AAA {[] [] [] [{GAA:[6]}, {CAA:[5]}] {5':[], ~5':[(5-0_0),(6-0_0)]} 2.0x}
-CAA {[{AAA:[5]}] [] [] [{ACA:[3]}] {5':[], ~5':[]} 2.0x}
-GAA {[{AAA:[6]}] [] [] [{AGA:[4]}] {5':[], ~5':[(4-0_0)]} 2.0x}
-TAA {[{AAG:[2]}, {AAC:[1]}] [] [] [] {5':[], ~5':[]} 2.0x}
-ACA {[{CAA:[3]}] [] [] [{AAC:[3]}] {5':[], ~5':[]} 1.0x}
-AGA {[{GAA:[4]}] [] [] [{AAG:[4]}] {5':[], ~5':[]} 1.0x}
-AAC {[{ACA:[3]}] [] [] [{TAA:[1]}] {5':[(3-0_0)], ~5':[(1-0_0)]} 2.0x}
-AAG {[{AGA:[4]}] [] [] [{TAA:[2]}] {5':[], ~5':[(2-0_0)]} 2.0x}
+AAA {[{AAG:[1]}] [] [] [{GAA:[1]}] {5':[], ~5':[]} 1.0x}
+GAA {[{AAA:[1]}] [] [] [{CGA:[1]}] {5':[], ~5':[]} 1.0x}
+CCA {[{CAG:[2]}] [] [] [{ACC:[2]}] {5':[], ~5':[]} 1.0x}
+CGA {[{GAA:[1]}] [] [{CGC:[1]}] [] {5':[], ~5':[]} 1.0x}
+ACC {[{CCA:[2]}] [{AGG:[1]}] [] [] {5':[], ~5':[]} 2.0x}
+GCC {[{CCG:[2]}] [] [] [{AGC:[2]}] {5':[], ~5':[]} 1.0x}
+AGC {[{GCC:[2]}] [] [] [{CAG:[2]}] {5':[], ~5':[]} 1.0x}
+CGC {[] [] [{CGA:[1]}] [{CCG:[2]}] {5':[], ~5':[(2-0_0),(1-0_0)]} 2.0x}
+AAG {[{AGG:[1]}] [] [] [{AAA:[1]}] {5':[], ~5':[]} 1.0x}
+CAG {[{AGC:[2]}] [] [] [{CCA:[2]}] {5':[], ~5':[]} 1.0x}
+CCG {[{CGC:[2]}] [] [] [{GCC:[2]}] {5':[], ~5':[]} 1.0x}
+AGG {[] [{ACC:[1]}] [] [{AAG:[1]}] {5':[], ~5':[]} 1.0x}
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoR/graphviz/result.ps b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoR/graphviz/result.ps
index 67e4fab..c338056 100644
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoR/graphviz/result.ps
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/RtoR/graphviz/result.ps
@@ -178,732 +178,1043 @@
%%EndSetup
setupLatin1
%%Page: 1 1
-%%PageBoundingBox: 36 36 1132 232
+%%PageBoundingBox: 36 36 1658 236
%%PageOrientation: Portrait
0 0 1 beginpage
gsave
-36 36 1096 196 boxprim clip newpath
+36 36 1622 200 boxprim clip newpath
1 1 set_scale 0 rotate 40 41 translate
% AAA
gsave
-0 0 0.75294 nodecolor
-newpath 0 6 moveto
-0 110 lineto
-78 110 lineto
-78 6 lineto
-closepath fill
1 setlinewidth
-filled
0 0 0 nodecolor
newpath 0 6 moveto
0 110 lineto
-78 110 lineto
-78 6 lineto
+56 110 lineto
+56 6 lineto
closepath stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-23.5 93.4 moveto 31 (AAA) alignedtext
+12.5 93.4 moveto 31 (AAA) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
newpath 0 84 moveto
-78 84 lineto
+56 84 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-25 67.4 moveto 28 (5':[]) alignedtext
+14 67.4 moveto 28 (5':[]) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
newpath 0 58 moveto
-78 58 lineto
+56 58 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-8 41.4 moveto 62 (~5':[5,6]) alignedtext
+8 41.4 moveto 40 (~5':[]) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
newpath 0 32 moveto
-78 32 lineto
+56 32 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-27.5 15.4 moveto 23 (2.0) alignedtext
+16.5 15.4 moveto 23 (1.0) alignedtext
+grestore
+% AAG
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 140 69 moveto
+140 173 lineto
+196 173 lineto
+196 69 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+152 156.4 moveto 32 (AAG) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 140 147 moveto
+196 147 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+154 130.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 140 121 moveto
+196 121 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+148 104.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 140 95 moveto
+196 95 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+156.5 78.4 moveto 23 (1.0) alignedtext
+grestore
+% AAA->AAG
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 56 85.12 moveto
+61.65 89.58 67.77 93.78 74 97 curveto
+91.26 105.91 112.06 111.67 129.69 115.3 curveto
+stroke
+0 0 0 edgecolor
+newpath 129.18 118.76 moveto
+139.66 117.2 lineto
+130.49 111.89 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 129.18 118.76 moveto
+139.66 117.2 lineto
+130.49 111.89 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+75.5 118.4 moveto 45 (FF: [1]) alignedtext
grestore
% GAA
gsave
-0 0 0.75294 nodecolor
-newpath 162.5 69 moveto
-162.5 173 lineto
-227.5 173 lineto
-227.5 69 lineto
-closepath fill
1 setlinewidth
-filled
0 0 0 nodecolor
-newpath 162.5 69 moveto
-162.5 173 lineto
-227.5 173 lineto
-227.5 69 lineto
+newpath 1558 7 moveto
+1558 111 lineto
+1614 111 lineto
+1614 7 lineto
closepath stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-179 156.4 moveto 32 (GAA) alignedtext
+1570 94.4 moveto 32 (GAA) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
-newpath 162.5 147 moveto
-227.5 147 lineto
+newpath 1558 85 moveto
+1614 85 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-181 130.4 moveto 28 (5':[]) alignedtext
+1572 68.4 moveto 28 (5':[]) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
-newpath 162.5 121 moveto
-227.5 121 lineto
+newpath 1558 59 moveto
+1614 59 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-170.5 104.4 moveto 49 (~5':[4]) alignedtext
+1566 42.4 moveto 40 (~5':[]) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
-newpath 162.5 95 moveto
-227.5 95 lineto
+newpath 1558 33 moveto
+1614 33 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-183.5 78.4 moveto 23 (2.0) alignedtext
+1574.5 16.4 moveto 23 (1.0) alignedtext
grestore
% AAA->GAA
gsave
1 setlinewidth
0 1 1 edgecolor
-newpath 78.1 87.41 moveto
-83.91 90.99 89.98 94.32 96 97 curveto
-113.77 104.92 134.56 110.46 152.48 114.21 curveto
+newpath 56.03 52.57 moveto
+84.21 47.6 128.95 41 168 41 curveto
+168 41 168 41 1446 41 curveto
+1480.66 41 1519.75 46.49 1547.8 51.41 curveto
stroke
0 1 1 edgecolor
-newpath 151.89 117.66 moveto
-162.38 116.16 lineto
-153.24 110.79 lineto
+newpath 1547.52 54.92 moveto
+1557.98 53.26 lineto
+1548.76 48.03 lineto
closepath fill
1 setlinewidth
solid
0 1 1 edgecolor
-newpath 151.89 117.66 moveto
-162.38 116.16 lineto
-153.24 110.79 lineto
+newpath 1547.52 54.92 moveto
+1557.98 53.26 lineto
+1548.76 48.03 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-96 117.4 moveto 48 (RR: [6]) alignedtext
+772 46.4 moveto 48 (RR: [1]) alignedtext
grestore
-% CAA
-gsave
-1 setlinewidth
-0 0 0 nodecolor
-newpath 1032 7 moveto
-1032 111 lineto
-1088 111 lineto
-1088 7 lineto
-closepath stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-1044.5 94.4 moveto 31 (CAA) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 1032 85 moveto
-1088 85 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-1046 68.4 moveto 28 (5':[]) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 1032 59 moveto
-1088 59 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-1040 42.4 moveto 40 (~5':[]) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 1032 33 moveto
-1088 33 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-1048.5 16.4 moveto 23 (2.0) alignedtext
-grestore
-% AAA->CAA
+% AAG->AAA
gsave
1 setlinewidth
0 1 1 edgecolor
-newpath 78.3 51.33 moveto
-109.77 46.57 155.09 41 195 41 curveto
-195 41 195 41 920 41 curveto
-954.66 41 993.75 46.49 1021.8 51.41 curveto
+newpath 139.99 87.84 moveto
+134.48 82.9 128.4 78.35 122 75 curveto
+104.93 66.06 83.99 61.74 66.21 59.68 curveto
stroke
0 1 1 edgecolor
-newpath 1021.52 54.92 moveto
-1031.98 53.26 lineto
-1022.76 48.03 lineto
+newpath 66.45 56.18 moveto
+56.16 58.71 lineto
+65.78 63.15 lineto
closepath fill
1 setlinewidth
solid
0 1 1 edgecolor
-newpath 1021.52 54.92 moveto
-1031.98 53.26 lineto
-1022.76 48.03 lineto
+newpath 66.45 56.18 moveto
+56.16 58.71 lineto
+65.78 63.15 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-536 46.4 moveto 48 (RR: [5]) alignedtext
+74 80.4 moveto 48 (RR: [1]) alignedtext
+grestore
+% AGG
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 280 88 moveto
+280 192 lineto
+336 192 lineto
+336 88 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+291.5 175.4 moveto 33 (AGG) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 280 166 moveto
+336 166 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+294 149.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 280 140 moveto
+336 140 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+288 123.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 280 114 moveto
+336 114 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+296.5 97.4 moveto 23 (1.0) alignedtext
+grestore
+% AAG->AGG
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 196.29 133.12 moveto
+202.05 135.11 208.14 136.89 214 138 curveto
+232.06 141.43 252.42 142.23 269.57 142.05 curveto
+stroke
+0 0 0 edgecolor
+newpath 269.86 145.54 moveto
+279.78 141.82 lineto
+269.7 138.54 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 269.86 145.54 moveto
+279.78 141.82 lineto
+269.7 138.54 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+215.5 147.4 moveto 45 (FF: [1]) alignedtext
grestore
% GAA->AAA
gsave
1 setlinewidth
0 0 0 edgecolor
-newpath 162.44 86.84 moveto
-156.68 82.26 150.45 78.09 144 75 curveto
-126.87 66.78 106.55 62.43 88.37 60.15 curveto
+newpath 1557.96 39.35 moveto
+1530.68 22.19 1487.41 0 1446 0 curveto
+168 0 168 0 168 0 curveto
+130.89 0 92.17 17.61 64.88 33.42 curveto
stroke
0 0 0 edgecolor
-newpath 88.56 56.65 moveto
-78.24 59.07 lineto
-87.81 63.61 lineto
+newpath 62.87 30.55 moveto
+56.09 38.69 lineto
+66.46 36.55 lineto
closepath fill
1 setlinewidth
solid
0 0 0 edgecolor
-newpath 88.56 56.65 moveto
-78.24 59.07 lineto
-87.81 63.61 lineto
+newpath 62.87 30.55 moveto
+56.09 38.69 lineto
+66.46 36.55 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-97.5 80.4 moveto 45 (FF: [6]) alignedtext
+773.5 5.4 moveto 45 (FF: [1]) alignedtext
grestore
-% AGA
+% CGA
gsave
1 setlinewidth
0 0 0 nodecolor
-newpath 312 80 moveto
-312 184 lineto
-368 184 lineto
-368 80 lineto
+newpath 1418 69 moveto
+1418 173 lineto
+1474 173 lineto
+1474 69 lineto
closepath stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-324.5 167.4 moveto 31 (AGA) alignedtext
+1430.5 156.4 moveto 31 (CGA) alignedtext
1 setlinewidth
0 0 0 nodecolor
-newpath 312 158 moveto
-368 158 lineto
+newpath 1418 147 moveto
+1474 147 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-326 141.4 moveto 28 (5':[]) alignedtext
+1432 130.4 moveto 28 (5':[]) alignedtext
1 setlinewidth
0 0 0 nodecolor
-newpath 312 132 moveto
-368 132 lineto
+newpath 1418 121 moveto
+1474 121 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-320 115.4 moveto 40 (~5':[]) alignedtext
+1426 104.4 moveto 40 (~5':[]) alignedtext
1 setlinewidth
0 0 0 nodecolor
-newpath 312 106 moveto
-368 106 lineto
+newpath 1418 95 moveto
+1474 95 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-328.5 89.4 moveto 23 (1.0) alignedtext
+1434.5 78.4 moveto 23 (1.0) alignedtext
grestore
-% GAA->AGA
+% GAA->CGA
gsave
1 setlinewidth
0 1 1 edgecolor
-newpath 227.55 127.51 moveto
-233.65 128.51 240 129.41 246 130 curveto
-264.3 131.8 284.69 132.4 301.79 132.51 curveto
+newpath 1557.97 61.07 moveto
+1538.57 63.41 1512.63 68.4 1492 79 curveto
+1488.68 80.71 1485.42 82.72 1482.26 84.92 curveto
stroke
0 1 1 edgecolor
-newpath 301.96 136.01 moveto
-311.96 132.53 lineto
-301.97 129.01 lineto
+newpath 1479.98 82.26 moveto
+1474.17 91.11 lineto
+1484.24 87.81 lineto
closepath fill
1 setlinewidth
solid
0 1 1 edgecolor
-newpath 301.96 136.01 moveto
-311.96 132.53 lineto
-301.97 129.01 lineto
+newpath 1479.98 82.26 moveto
+1474.17 91.11 lineto
+1484.24 87.81 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-246 137.4 moveto 48 (RR: [4]) alignedtext
+1492 84.4 moveto 48 (RR: [1]) alignedtext
grestore
-% CAA->AAA
+% CGA->GAA
gsave
1 setlinewidth
0 0 0 edgecolor
-newpath 1031.96 39.35 moveto
-1004.68 22.19 961.41 0 920 0 curveto
-195 0 195 0 195 0 curveto
-157.16 0 117.21 15.18 87.22 30 curveto
+newpath 1474.3 117.12 moveto
+1493.58 113.68 1519.28 107.53 1540 97 curveto
+1543.29 95.33 1546.55 93.39 1549.73 91.29 curveto
stroke
0 0 0 edgecolor
-newpath 85.56 26.92 moveto
-78.24 34.58 lineto
-88.74 33.16 lineto
+newpath 1551.83 94.08 moveto
+1557.92 85.41 lineto
+1547.75 88.4 lineto
closepath fill
1 setlinewidth
solid
0 0 0 edgecolor
-newpath 85.56 26.92 moveto
-78.24 34.58 lineto
-88.74 33.16 lineto
+newpath 1551.83 94.08 moveto
+1557.92 85.41 lineto
+1547.75 88.4 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-537.5 5.4 moveto 45 (FF: [5]) alignedtext
+1493.5 118.4 moveto 45 (FF: [1]) alignedtext
grestore
-% ACA
-gsave
-1 setlinewidth
-0 0 0 nodecolor
-newpath 892 69 moveto
-892 173 lineto
-948 173 lineto
-948 69 lineto
-closepath stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-905 156.4 moveto 30 (ACA) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 892 147 moveto
-948 147 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-906 130.4 moveto 28 (5':[]) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 892 121 moveto
-948 121 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-900 104.4 moveto 40 (~5':[]) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 892 95 moveto
-948 95 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-908.5 78.4 moveto 23 (1.0) alignedtext
-grestore
-% CAA->ACA
-gsave
-1 setlinewidth
-0 1 1 edgecolor
-newpath 1031.97 61.07 moveto
-1012.57 63.41 986.63 68.4 966 79 curveto
-962.68 80.71 959.42 82.72 956.26 84.92 curveto
-stroke
-0 1 1 edgecolor
-newpath 953.98 82.26 moveto
-948.17 91.11 lineto
-958.24 87.81 lineto
-closepath fill
-1 setlinewidth
-solid
-0 1 1 edgecolor
-newpath 953.98 82.26 moveto
-948.17 91.11 lineto
-958.24 87.81 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-966 84.4 moveto 48 (RR: [3]) alignedtext
-grestore
-% ACA->CAA
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 948.3 117.12 moveto
-967.58 113.68 993.28 107.53 1014 97 curveto
-1017.29 95.33 1020.55 93.39 1023.73 91.29 curveto
-stroke
-0 0 0 edgecolor
-newpath 1025.83 94.08 moveto
-1031.92 85.41 lineto
-1021.75 88.4 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 1025.83 94.08 moveto
-1031.92 85.41 lineto
-1021.75 88.4 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-967.5 118.4 moveto 45 (FF: [3]) alignedtext
-grestore
-% AAC
+% CGC
gsave
0 0 0.75294 nodecolor
-newpath 742.5 74 moveto
-742.5 178 lineto
-807.5 178 lineto
-807.5 74 lineto
+newpath 1258 70 moveto
+1258 174 lineto
+1336 174 lineto
+1336 70 lineto
closepath fill
1 setlinewidth
filled
0 0 0 nodecolor
-newpath 742.5 74 moveto
-742.5 178 lineto
-807.5 178 lineto
-807.5 74 lineto
+newpath 1258 70 moveto
+1258 174 lineto
+1336 174 lineto
+1336 70 lineto
closepath stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-759.5 161.4 moveto 31 (AAC) alignedtext
+1281.5 157.4 moveto 31 (CGC) alignedtext
1 setlinewidth
filled
0 0 0 nodecolor
-newpath 742.5 152 moveto
-807.5 152 lineto
+newpath 1258 148 moveto
+1336 148 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-756.5 135.4 moveto 37 (5':[3]) alignedtext
+1283 131.4 moveto 28 (5':[]) alignedtext
1 setlinewidth
filled
0 0 0 nodecolor
-newpath 742.5 126 moveto
-807.5 126 lineto
+newpath 1258 122 moveto
+1336 122 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-750.5 109.4 moveto 49 (~5':[1]) alignedtext
+1266 105.4 moveto 62 (~5':[2,1]) alignedtext
1 setlinewidth
filled
0 0 0 nodecolor
-newpath 742.5 100 moveto
-807.5 100 lineto
+newpath 1258 96 moveto
+1336 96 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-763.5 83.4 moveto 23 (2.0) alignedtext
+1285.5 79.4 moveto 23 (2.0) alignedtext
grestore
-% ACA->AAC
+% CGA->CGC
gsave
1 setlinewidth
-0 1 1 edgecolor
-newpath 891.97 95.28 moveto
-886.37 91.47 880.28 88.12 874 86 curveto
-853.78 79.18 846.16 79.04 826 86 curveto
-822.71 87.14 819.47 88.58 816.32 90.25 curveto
+0.33333 1 1 edgecolor
+newpath 1417.8 91.99 moveto
+1412.31 87.9 1406.29 84.31 1400 82 curveto
+1380.81 74.96 1373.5 75.84 1354 82 curveto
+1351.04 82.93 1348.1 84.08 1345.21 85.4 curveto
stroke
-0 1 1 edgecolor
-newpath 814.45 87.28 moveto
-807.69 95.44 lineto
-818.06 93.28 lineto
+0.33333 1 1 edgecolor
+newpath 1343.43 82.37 moveto
+1336.16 90.07 lineto
+1346.65 88.59 lineto
closepath fill
1 setlinewidth
solid
-0 1 1 edgecolor
-newpath 814.45 87.28 moveto
-807.69 95.44 lineto
-818.06 93.28 lineto
+0.33333 1 1 edgecolor
+newpath 1343.43 82.37 moveto
+1336.16 90.07 lineto
+1346.65 88.59 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-826 91.4 moveto 48 (RR: [3]) alignedtext
+1354 87.4 moveto 46 (RF: [1]) alignedtext
grestore
-% AGA->GAA
+% CCA
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 558 73 moveto
+558 177 lineto
+614 177 lineto
+614 73 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+571 160.4 moveto 30 (CCA) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 558 151 moveto
+614 151 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+572 134.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 558 125 moveto
+614 125 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+566 108.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 558 99 moveto
+614 99 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+574.5 82.4 moveto 23 (1.0) alignedtext
+grestore
+% CAG
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 698 70 moveto
+698 174 lineto
+754 174 lineto
+754 70 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+710.5 157.4 moveto 31 (CAG) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 698 148 moveto
+754 148 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+712 131.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 698 122 moveto
+754 122 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+706 105.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 698 96 moveto
+754 96 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+714.5 79.4 moveto 23 (1.0) alignedtext
+grestore
+% CCA->CAG
gsave
1 setlinewidth
0 0 0 edgecolor
-newpath 311.64 114.54 moveto
-305.98 111.84 299.95 109.46 294 108 curveto
-275.84 103.55 255.42 105.15 237.86 108.5 curveto
+newpath 614.33 124.39 moveto
+635.39 123.94 664.37 123.32 687.53 122.82 curveto
stroke
0 0 0 edgecolor
-newpath 236.93 105.12 moveto
-227.88 110.64 lineto
-238.4 111.97 lineto
+newpath 687.79 126.32 moveto
+697.71 122.61 lineto
+687.64 119.32 lineto
closepath fill
1 setlinewidth
solid
0 0 0 edgecolor
-newpath 236.93 105.12 moveto
-227.88 110.64 lineto
-238.4 111.97 lineto
+newpath 687.79 126.32 moveto
+697.71 122.61 lineto
+687.64 119.32 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-247.5 113.4 moveto 45 (FF: [4]) alignedtext
+633.5 128.4 moveto 45 (FF: [2]) alignedtext
grestore
-% AAG
+% ACC
gsave
-0 0 0.75294 nodecolor
-newpath 452.5 70 moveto
-452.5 174 lineto
-517.5 174 lineto
-517.5 70 lineto
-closepath fill
1 setlinewidth
-filled
0 0 0 nodecolor
-newpath 452.5 70 moveto
-452.5 174 lineto
-517.5 174 lineto
-517.5 70 lineto
+newpath 418 78 moveto
+418 182 lineto
+474 182 lineto
+474 78 lineto
closepath stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-469 157.4 moveto 32 (AAG) alignedtext
+431 165.4 moveto 30 (ACC) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
-newpath 452.5 148 moveto
-517.5 148 lineto
+newpath 418 156 moveto
+474 156 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-471 131.4 moveto 28 (5':[]) alignedtext
+432 139.4 moveto 28 (5':[]) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
-newpath 452.5 122 moveto
-517.5 122 lineto
+newpath 418 130 moveto
+474 130 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-460.5 105.4 moveto 49 (~5':[2]) alignedtext
+426 113.4 moveto 40 (~5':[]) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
-newpath 452.5 96 moveto
-517.5 96 lineto
+newpath 418 104 moveto
+474 104 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-473.5 79.4 moveto 23 (2.0) alignedtext
+434.5 87.4 moveto 23 (2.0) alignedtext
grestore
-% AGA->AAG
+% CCA->ACC
gsave
1 setlinewidth
0 1 1 edgecolor
-newpath 368.3 130.05 moveto
-389.34 128.6 418.4 126.59 442.26 124.95 curveto
+newpath 557.97 99.28 moveto
+552.37 95.47 546.28 92.12 540 90 curveto
+519.78 83.18 511.98 82.53 492 90 curveto
+488.73 91.22 485.54 92.8 482.46 94.61 curveto
stroke
0 1 1 edgecolor
-newpath 442.73 128.42 moveto
-452.47 124.24 lineto
-442.25 121.44 lineto
+newpath 480.43 91.75 moveto
+474.11 100.25 lineto
+484.35 97.55 lineto
closepath fill
1 setlinewidth
solid
0 1 1 edgecolor
-newpath 442.73 128.42 moveto
-452.47 124.24 lineto
-442.25 121.44 lineto
+newpath 480.43 91.75 moveto
+474.11 100.25 lineto
+484.35 97.55 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-386 133.4 moveto 48 (RR: [4]) alignedtext
+492 95.4 moveto 48 (RR: [2]) alignedtext
grestore
-% TAA
-gsave
-1 setlinewidth
-0 0 0 nodecolor
-newpath 602 84 moveto
-602 188 lineto
-658 188 lineto
-658 84 lineto
-closepath stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-615.5 171.4 moveto 29 (TAA) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 602 162 moveto
-658 162 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-616 145.4 moveto 28 (5':[]) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 602 136 moveto
-658 136 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-610 119.4 moveto 40 (~5':[]) alignedtext
-1 setlinewidth
-0 0 0 nodecolor
-newpath 602 110 moveto
-658 110 lineto
-stroke
-0 0 0 nodecolor
-14 /Times-Roman set_font
-618.5 93.4 moveto 23 (2.0) alignedtext
-grestore
-% TAA->AAG
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 601.88 111 moveto
-596.3 107.3 590.23 104.05 584 102 curveto
-565.73 95.98 544.94 98.79 527.15 103.97 curveto
-stroke
-0 0 0 edgecolor
-newpath 526.05 100.65 moveto
-517.61 107.05 lineto
-528.2 107.31 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 526.05 100.65 moveto
-517.61 107.05 lineto
-528.2 107.31 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-537.5 107.4 moveto 45 (FF: [2]) alignedtext
-grestore
-% TAA->AAC
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 658.3 134.05 moveto
-679.34 132.6 708.4 130.59 732.26 128.95 curveto
-stroke
-0 0 0 edgecolor
-newpath 732.73 132.42 moveto
-742.47 128.24 lineto
-732.25 125.44 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 732.73 132.42 moveto
-742.47 128.24 lineto
-732.25 125.44 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-677.5 137.4 moveto 45 (FF: [1]) alignedtext
-grestore
-% AAG->AGA
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 452.29 107.87 moveto
-446.31 105.85 440.04 104.09 434 103 curveto
-413 99.22 406.5 97.08 386 103 curveto
-383.01 103.86 380.03 104.98 377.11 106.28 curveto
-stroke
-0 0 0 edgecolor
-newpath 375.32 103.27 moveto
-368.01 110.93 lineto
-378.51 109.5 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 375.32 103.27 moveto
-368.01 110.93 lineto
-378.51 109.5 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-387.5 108.4 moveto 45 (FF: [4]) alignedtext
-grestore
-% AAG->TAA
+% CAG->CCA
gsave
1 setlinewidth
0 1 1 edgecolor
-newpath 517.54 125.14 moveto
-539.55 127.27 568.71 130.08 591.82 132.31 curveto
+newpath 697.95 106.92 moveto
+692.17 104.47 686 102.31 680 101 curveto
+659.15 96.47 652.72 95.92 632 101 curveto
+629.21 101.68 626.4 102.57 623.63 103.6 curveto
stroke
0 1 1 edgecolor
-newpath 591.68 135.82 moveto
-601.97 133.29 lineto
-592.35 128.85 lineto
+newpath 622.19 100.4 moveto
+614.36 107.54 lineto
+624.93 106.84 lineto
closepath fill
1 setlinewidth
solid
0 1 1 edgecolor
-newpath 591.68 135.82 moveto
-601.97 133.29 lineto
-592.35 128.85 lineto
+newpath 622.19 100.4 moveto
+614.36 107.54 lineto
+624.93 106.84 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-536 136.4 moveto 48 (RR: [2]) alignedtext
+632 106.4 moveto 48 (RR: [2]) alignedtext
grestore
-% AAC->ACA
+% AGC
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 838 88 moveto
+838 192 lineto
+894 192 lineto
+894 88 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+850.5 175.4 moveto 31 (AGC) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 838 166 moveto
+894 166 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+852 149.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 838 140 moveto
+894 140 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+846 123.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 838 114 moveto
+894 114 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+854.5 97.4 moveto 23 (1.0) alignedtext
+grestore
+% CAG->AGC
gsave
1 setlinewidth
0 0 0 edgecolor
-newpath 807.54 124.88 moveto
-829.55 124.12 858.71 123.11 881.82 122.32 curveto
+newpath 754.33 125.64 moveto
+775.39 128.35 804.37 132.08 827.53 135.05 curveto
stroke
0 0 0 edgecolor
-newpath 882.09 125.81 moveto
-891.97 121.97 lineto
-881.85 118.81 lineto
+newpath 827.35 138.56 moveto
+837.71 136.36 lineto
+828.24 131.62 lineto
closepath fill
1 setlinewidth
solid
0 0 0 edgecolor
-newpath 882.09 125.81 moveto
-891.97 121.97 lineto
-881.85 118.81 lineto
+newpath 827.35 138.56 moveto
+837.71 136.36 lineto
+828.24 131.62 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-827.5 129.4 moveto 45 (FF: [3]) alignedtext
+773.5 138.4 moveto 45 (FF: [2]) alignedtext
grestore
-% AAC->TAA
+% ACC->CCA
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 474.33 128.99 moveto
+495.39 128.24 524.37 127.2 547.53 126.37 curveto
+stroke
+0 0 0 edgecolor
+newpath 547.84 129.87 moveto
+557.71 126.01 lineto
+547.59 122.87 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 547.84 129.87 moveto
+557.71 126.01 lineto
+547.59 122.87 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+493.5 133.4 moveto 45 (FF: [2]) alignedtext
+grestore
+% ACC->AGG
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 417.82 108.07 moveto
+412.19 104.74 406.12 101.82 400 100 curveto
+380.4 94.17 373.15 92.84 354 100 curveto
+350.73 101.22 347.54 102.8 344.46 104.61 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 342.43 101.75 moveto
+336.11 110.25 lineto
+346.35 107.55 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 342.43 101.75 moveto
+336.11 110.25 lineto
+346.35 107.55 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+354 105.4 moveto 46 (FR: [1]) alignedtext
+grestore
+% CGC->CGA
+gsave
+1 setlinewidth
+0.33333 1 1 edgecolor
+newpath 1336.15 121.74 moveto
+1358.23 121.59 1385.7 121.4 1407.65 121.26 curveto
+stroke
+0.33333 1 1 edgecolor
+newpath 1407.96 124.76 moveto
+1417.94 121.19 lineto
+1407.91 117.76 lineto
+closepath fill
+1 setlinewidth
+solid
+0.33333 1 1 edgecolor
+newpath 1407.96 124.76 moveto
+1417.94 121.19 lineto
+1407.91 117.76 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+1354 126.4 moveto 46 (RF: [1]) alignedtext
+grestore
+% CCG
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1118 73 moveto
+1118 177 lineto
+1174 177 lineto
+1174 73 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1130.5 160.4 moveto 31 (CCG) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1118 151 moveto
+1174 151 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1132 134.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1118 125 moveto
+1174 125 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1126 108.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 1118 99 moveto
+1174 99 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+1134.5 82.4 moveto 23 (1.0) alignedtext
+grestore
+% CGC->CCG
gsave
1 setlinewidth
0 1 1 edgecolor
-newpath 742.29 111.87 moveto
-736.31 109.85 730.04 108.09 724 107 curveto
-703 103.22 696.5 101.08 676 107 curveto
-673.01 107.86 670.03 108.98 667.11 110.28 curveto
+newpath 1257.95 92.62 moveto
+1252.18 89.5 1246.11 86.81 1240 85 curveto
+1219.54 78.94 1211.98 77.53 1192 85 curveto
+1188.73 86.22 1185.54 87.8 1182.46 89.61 curveto
stroke
0 1 1 edgecolor
-newpath 665.32 107.27 moveto
-658.01 114.93 lineto
-668.51 113.5 lineto
+newpath 1180.43 86.75 moveto
+1174.11 95.25 lineto
+1184.35 92.55 lineto
closepath fill
1 setlinewidth
solid
0 1 1 edgecolor
-newpath 665.32 107.27 moveto
-658.01 114.93 lineto
-668.51 113.5 lineto
+newpath 1180.43 86.75 moveto
+1174.11 95.25 lineto
+1184.35 92.55 lineto
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-676 112.4 moveto 48 (RR: [1]) alignedtext
+1192 90.4 moveto 48 (RR: [2]) alignedtext
+grestore
+% AGG->AAG
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 279.64 122.54 moveto
+273.98 119.84 267.95 117.46 262 116 curveto
+244.12 111.62 223.78 112.06 206.61 113.93 curveto
+stroke
+0 1 1 edgecolor
+newpath 205.84 110.5 moveto
+196.37 115.25 lineto
+206.74 117.44 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 205.84 110.5 moveto
+196.37 115.25 lineto
+206.74 117.44 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+214 121.4 moveto 48 (RR: [1]) alignedtext
+grestore
+% AGG->ACC
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 336.26 137.95 moveto
+356.82 136.46 384.89 134.43 407.5 132.79 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 408.06 136.26 moveto
+417.78 132.05 lineto
+407.55 129.28 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 408.06 136.26 moveto
+417.78 132.05 lineto
+407.55 129.28 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+354 141.4 moveto 46 (FR: [1]) alignedtext
+grestore
+% GCC
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 978 78 moveto
+978 182 lineto
+1034 182 lineto
+1034 78 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+990.5 165.4 moveto 31 (GCC) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 978 156 moveto
+1034 156 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+992 139.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 978 130 moveto
+1034 130 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+986 113.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 978 104 moveto
+1034 104 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+994.5 87.4 moveto 23 (1.0) alignedtext
+grestore
+% GCC->CCG
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 1034.33 128.99 moveto
+1055.39 128.24 1084.37 127.2 1107.53 126.37 curveto
+stroke
+0 0 0 edgecolor
+newpath 1107.84 129.87 moveto
+1117.71 126.01 lineto
+1107.59 122.87 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 1107.84 129.87 moveto
+1117.71 126.01 lineto
+1107.59 122.87 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+1053.5 133.4 moveto 45 (FF: [2]) alignedtext
+grestore
+% GCC->AGC
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 977.82 108.07 moveto
+972.19 104.74 966.12 101.82 960 100 curveto
+939.55 93.92 931.98 92.53 912 100 curveto
+908.73 101.22 905.54 102.8 902.46 104.61 curveto
+stroke
+0 1 1 edgecolor
+newpath 900.43 101.75 moveto
+894.11 110.25 lineto
+904.35 107.55 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 900.43 101.75 moveto
+894.11 110.25 lineto
+904.35 107.55 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+912 105.4 moveto 48 (RR: [2]) alignedtext
+grestore
+% CCG->CGC
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 1174.05 124.44 moveto
+1194.65 124.03 1223.17 123.47 1247.55 122.98 curveto
+stroke
+0 0 0 edgecolor
+newpath 1247.79 126.48 moveto
+1257.72 122.78 lineto
+1247.65 119.48 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 1247.79 126.48 moveto
+1257.72 122.78 lineto
+1247.65 119.48 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+1193.5 129.4 moveto 45 (FF: [2]) alignedtext
+grestore
+% CCG->GCC
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 1117.95 109.92 moveto
+1112.17 107.47 1106 105.31 1100 104 curveto
+1079.15 99.47 1072.63 98.57 1052 104 curveto
+1049.17 104.74 1046.34 105.71 1043.54 106.82 curveto
+stroke
+0 1 1 edgecolor
+newpath 1041.85 103.74 moveto
+1034.23 111.1 lineto
+1044.77 110.1 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 1041.85 103.74 moveto
+1034.23 111.1 lineto
+1044.77 110.1 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+1052 109.4 moveto 48 (RR: [2]) alignedtext
+grestore
+% AGC->CAG
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 837.97 111.91 moveto
+832.42 107.85 826.34 104.28 820 102 curveto
+799.93 94.78 792.89 97.66 772 102 curveto
+769.2 102.58 766.37 103.34 763.55 104.23 curveto
+stroke
+0 1 1 edgecolor
+newpath 762.33 100.95 moveto
+754.11 107.63 lineto
+764.71 107.53 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 762.33 100.95 moveto
+754.11 107.63 lineto
+764.71 107.53 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+772 107.4 moveto 48 (RR: [2]) alignedtext
+grestore
+% AGC->GCC
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 894.33 137.98 moveto
+915.39 136.47 944.37 134.4 967.53 132.75 curveto
+stroke
+0 0 0 edgecolor
+newpath 967.99 136.22 moveto
+977.71 132.02 lineto
+967.49 129.24 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 967.99 136.22 moveto
+977.71 132.02 lineto
+967.49 129.24 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+913.5 141.4 moveto 45 (FF: [2]) alignedtext
grestore
endpage
showpage
@@ -912,7 +1223,7 @@
%%EndPage: 1
%%Trailer
%%Pages: 1
-%%BoundingBox: 36 36 1132 232
+%%BoundingBox: 36 36 1658 236
end
restore
%%EOF
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/SimpleBubble/..binmerge.crc b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/SimpleBubble/..binmerge.crc
index 53a3c87..f7663be 100644
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/SimpleBubble/..binmerge.crc
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/SimpleBubble/..binmerge.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/SimpleBubble/.binmerge b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/SimpleBubble/.binmerge
index 7ebdfbd..7d6525f 100755
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/SimpleBubble/.binmerge
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/SimpleBubble/.binmerge
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/SimpleBubble/bin/.part-00000.crc b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/SimpleBubble/bin/.part-00000.crc
index c55a6e0..a0f8bf6 100644
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/SimpleBubble/bin/.part-00000.crc
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/SimpleBubble/bin/.part-00000.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/SimpleBubble/bin/part-00000 b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/SimpleBubble/bin/part-00000
index 7f56986..24928f9 100755
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/SimpleBubble/bin/part-00000
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/SimpleBubble/bin/part-00000
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/SimpleBubble/data b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/SimpleBubble/data
index 47d1b71..2636c37 100644
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/SimpleBubble/data
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/SimpleBubble/data
@@ -1,8 +1,8 @@
-AAA {[] [] [] [{GAA:[6]}, {CAA:[5]}] {5':[], ~5':[]} 2.0x}
-CAA {[{AAA:[5]}] [] [] [{ACA:[3]}] {5':[(5-0_0)], ~5':[]} 2.0x}
-GAA {[{AAA:[6]}] [] [] [{AGA:[4]}] {5':[(6-0_0)], ~5':[]} 2.0x}
+AAA {[] [] [] [{GAA:[2]}, {CAA:[1]}] {5':[], ~5':[]} 2.0x}
+CAA {[{AAA:[1]}] [] [] [{ACA:[1]}] {5':[], ~5':[]} 1.0x}
+GAA {[{AAA:[2]}] [] [] [{AGA:[2]}] {5':[], ~5':[]} 1.0x}
TAA {[{AAG:[2]}, {AAC:[1]}] [] [] [] {5':[(2-0_0),(1-0_0)], ~5':[]} 2.0x}
-ACA {[{CAA:[3]}] [] [] [{AAC:[3]}] {5':[], ~5':[]} 1.0x}
-AGA {[{GAA:[4]}] [] [] [{AAG:[4]}] {5':[], ~5':[]} 1.0x}
-AAC {[{ACA:[3]}] [] [] [{TAA:[1]}] {5':[(3-0_0)], ~5':[]} 2.0x}
-AAG {[{AGA:[4]}] [] [] [{TAA:[2]}] {5':[(4-0_0)], ~5':[]} 2.0x}
+ACA {[{CAA:[1]}] [] [] [{AAC:[1]}] {5':[], ~5':[]} 1.0x}
+AGA {[{GAA:[2]}] [] [] [{AAG:[2]}] {5':[], ~5':[]} 1.0x}
+AAC {[{ACA:[1]}] [] [] [{TAA:[1]}] {5':[], ~5':[]} 1.0x}
+AAG {[{AGA:[2]}] [] [] [{TAA:[2]}] {5':[], ~5':[]} 1.0x}
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/SimpleBubble/graphviz/result.ps b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/SimpleBubble/graphviz/result.ps
index a5611b0..33834ad 100644
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/SimpleBubble/graphviz/result.ps
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/BubbleMerge_Input/SimpleBubble/graphviz/result.ps
@@ -223,14 +223,7 @@
grestore
% GAA
gsave
-0 0 0.75294 nodecolor
-newpath 140 69 moveto
-140 173 lineto
-196 173 lineto
-196 69 lineto
-closepath fill
1 setlinewidth
-filled
0 0 0 nodecolor
newpath 140 69 moveto
140 173 lineto
@@ -241,16 +234,14 @@
14 /Times-Roman set_font
152 156.4 moveto 32 (GAA) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
newpath 140 147 moveto
196 147 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-149.5 130.4 moveto 37 (5':[6]) alignedtext
+154 130.4 moveto 28 (5':[]) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
newpath 140 121 moveto
196 121 lineto
@@ -259,14 +250,13 @@
14 /Times-Roman set_font
148 104.4 moveto 40 (~5':[]) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
newpath 140 95 moveto
196 95 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-156.5 78.4 moveto 23 (2.0) alignedtext
+156.5 78.4 moveto 23 (1.0) alignedtext
grestore
% AAA->GAA
gsave
@@ -290,18 +280,11 @@
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-74 118.4 moveto 48 (RR: [6]) alignedtext
+74 118.4 moveto 48 (RR: [2]) alignedtext
grestore
% CAA
gsave
-0 0 0.75294 nodecolor
-newpath 990 7 moveto
-990 111 lineto
-1046 111 lineto
-1046 7 lineto
-closepath fill
1 setlinewidth
-filled
0 0 0 nodecolor
newpath 990 7 moveto
990 111 lineto
@@ -312,16 +295,14 @@
14 /Times-Roman set_font
1002.5 94.4 moveto 31 (CAA) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
newpath 990 85 moveto
1046 85 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-999.5 68.4 moveto 37 (5':[5]) alignedtext
+1004 68.4 moveto 28 (5':[]) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
newpath 990 59 moveto
1046 59 lineto
@@ -330,14 +311,13 @@
14 /Times-Roman set_font
998 42.4 moveto 40 (~5':[]) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
newpath 990 33 moveto
1046 33 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-1006.5 16.4 moveto 23 (2.0) alignedtext
+1006.5 16.4 moveto 23 (1.0) alignedtext
grestore
% AAA->CAA
gsave
@@ -362,7 +342,7 @@
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-494 46.4 moveto 48 (RR: [5]) alignedtext
+494 46.4 moveto 48 (RR: [1]) alignedtext
grestore
% GAA->AAA
gsave
@@ -386,7 +366,7 @@
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-75.5 80.4 moveto 45 (FF: [6]) alignedtext
+75.5 80.4 moveto 45 (FF: [2]) alignedtext
grestore
% AGA
gsave
@@ -447,7 +427,7 @@
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-214 137.4 moveto 48 (RR: [4]) alignedtext
+214 137.4 moveto 48 (RR: [2]) alignedtext
grestore
% CAA->AAA
gsave
@@ -472,7 +452,7 @@
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-495.5 5.4 moveto 45 (FF: [5]) alignedtext
+495.5 5.4 moveto 45 (FF: [1]) alignedtext
grestore
% ACA
gsave
@@ -533,7 +513,7 @@
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-924 84.4 moveto 48 (RR: [3]) alignedtext
+924 84.4 moveto 48 (RR: [1]) alignedtext
grestore
% ACA->CAA
gsave
@@ -557,18 +537,11 @@
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-925.5 118.4 moveto 45 (FF: [3]) alignedtext
+925.5 118.4 moveto 45 (FF: [1]) alignedtext
grestore
% AAC
gsave
-0 0 0.75294 nodecolor
-newpath 710 74 moveto
-710 178 lineto
-766 178 lineto
-766 74 lineto
-closepath fill
1 setlinewidth
-filled
0 0 0 nodecolor
newpath 710 74 moveto
710 178 lineto
@@ -579,16 +552,14 @@
14 /Times-Roman set_font
722.5 161.4 moveto 31 (AAC) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
newpath 710 152 moveto
766 152 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-719.5 135.4 moveto 37 (5':[3]) alignedtext
+724 135.4 moveto 28 (5':[]) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
newpath 710 126 moveto
766 126 lineto
@@ -597,14 +568,13 @@
14 /Times-Roman set_font
718 109.4 moveto 40 (~5':[]) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
newpath 710 100 moveto
766 100 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-726.5 83.4 moveto 23 (2.0) alignedtext
+726.5 83.4 moveto 23 (1.0) alignedtext
grestore
% ACA->AAC
gsave
@@ -629,7 +599,7 @@
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-784 91.4 moveto 48 (RR: [3]) alignedtext
+784 91.4 moveto 48 (RR: [1]) alignedtext
grestore
% AGA->GAA
gsave
@@ -653,18 +623,11 @@
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-215.5 113.4 moveto 45 (FF: [4]) alignedtext
+215.5 113.4 moveto 45 (FF: [2]) alignedtext
grestore
% AAG
gsave
-0 0 0.75294 nodecolor
-newpath 420 70 moveto
-420 174 lineto
-476 174 lineto
-476 70 lineto
-closepath fill
1 setlinewidth
-filled
0 0 0 nodecolor
newpath 420 70 moveto
420 174 lineto
@@ -675,16 +638,14 @@
14 /Times-Roman set_font
432 157.4 moveto 32 (AAG) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
newpath 420 148 moveto
476 148 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-429.5 131.4 moveto 37 (5':[4]) alignedtext
+434 131.4 moveto 28 (5':[]) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
newpath 420 122 moveto
476 122 lineto
@@ -693,14 +654,13 @@
14 /Times-Roman set_font
428 105.4 moveto 40 (~5':[]) alignedtext
1 setlinewidth
-filled
0 0 0 nodecolor
newpath 420 96 moveto
476 96 lineto
stroke
0 0 0 nodecolor
14 /Times-Roman set_font
-436.5 79.4 moveto 23 (2.0) alignedtext
+436.5 79.4 moveto 23 (1.0) alignedtext
grestore
% AGA->AAG
gsave
@@ -723,7 +683,7 @@
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-354 133.4 moveto 48 (RR: [4]) alignedtext
+354 133.4 moveto 48 (RR: [2]) alignedtext
grestore
% TAA
gsave
@@ -843,7 +803,7 @@
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-355.5 108.4 moveto 45 (FF: [4]) alignedtext
+355.5 108.4 moveto 45 (FF: [2]) alignedtext
grestore
% AAG->TAA
gsave
@@ -889,7 +849,7 @@
closepath stroke
0 0 0 edgecolor
14 /Times-Roman set_font
-785.5 129.4 moveto 45 (FF: [3]) alignedtext
+785.5 129.4 moveto 45 (FF: [1]) alignedtext
grestore
% AAC->TAA
gsave
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/BubbleMergeMessageWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/BubbleMergeMessageWritable.java
index 9585608..b8ff5fd 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/BubbleMergeMessageWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/BubbleMergeMessageWritable.java
@@ -5,6 +5,7 @@
import java.io.IOException;
import java.util.Comparator;
+import edu.uci.ics.genomix.pregelix.type.MessageFlag;
import edu.uci.ics.genomix.type.NodeWritable;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
@@ -18,12 +19,14 @@
private VKmerBytesWritable majorVertexId; //use for MergeBubble
private NodeWritable node; //except kmer, other field should be updated when MergeBubble
private byte meToMajorDir;
+ private byte meToMinorDir;
public BubbleMergeMessageWritable(){
super();
majorVertexId = new VKmerBytesWritable();
node = new NodeWritable();
meToMajorDir = 0;
+ meToMinorDir = 0;
}
public void set(BubbleMergeMessageWritable msg){
@@ -31,7 +34,8 @@
this.setFlag(msg.getFlag());
this.setMajorVertexId(msg.getMajorVertexId());
this.setNode(msg.node);
- this.setMeToMajorDir(meToMajorDir);
+ this.setMeToMajorDir(msg.meToMajorDir);
+ this.setMeToMinorDir(msg.meToMinorDir);
}
public void reset(){
@@ -39,6 +43,19 @@
majorVertexId.reset(0);
node.reset();
meToMajorDir = 0;
+ meToMinorDir = 0;
+ }
+
+ public byte getRelativeDirToMajor(){
+ switch(meToMajorDir){
+ case MessageFlag.DIR_FF:
+ case MessageFlag.DIR_RR:
+ return DirToMajor.FORWARD;
+ case MessageFlag.DIR_FR:
+ case MessageFlag.DIR_RF:
+ return DirToMajor.REVERSE;
+ }
+ return 0;
}
public VKmerBytesWritable getMajorVertexId() {
@@ -54,7 +71,7 @@
}
public void setNode(NodeWritable node) {
- this.node = node;
+ this.node.setAsCopy(node);
}
public byte getMeToMajorDir() {
@@ -65,6 +82,14 @@
this.meToMajorDir = meToMajorDir;
}
+ public byte getMeToMinorDir() {
+ return meToMinorDir;
+ }
+
+ public void setMeToMinorDir(byte meToMinorDir) {
+ this.meToMinorDir = meToMinorDir;
+ }
+
@Override
public void readFields(DataInput in) throws IOException {
reset();
@@ -72,6 +97,7 @@
majorVertexId.readFields(in);
node.readFields(in);
meToMajorDir = in.readByte();
+ meToMinorDir = in.readByte();
}
@Override
@@ -80,6 +106,7 @@
majorVertexId.write(out);
node.write(out);
out.writeByte(meToMajorDir);
+ out.write(meToMinorDir);
}
public static class SortByCoverage implements Comparator<BubbleMergeMessageWritable> {
@@ -90,13 +117,13 @@
}
public float computeDissimilar(BubbleMergeMessageWritable other){
- if(this.getMeToMajorDir() == other.getMeToMajorDir())
- return this.getSourceVertexId().fracDissimilar(other.getSourceVertexId());
+ if(this.getRelativeDirToMajor() == other.getRelativeDirToMajor())
+ return this.getNode().getInternalKmer().fracDissimilar(other.getNode().getInternalKmer());
else{
- String reverse = other.getSourceVertexId().toString();
+ String reverse = other.getNode().getInternalKmer().toString();
VKmerBytesWritable reverseKmer = new VKmerBytesWritable();
reverseKmer.setByReadReverse(reverse.length(), reverse.getBytes(), 0);
- return this.getSourceVertexId().fracDissimilar(reverseKmer);
+ return this.getNode().getInternalKmer().fracDissimilar(reverseKmer);
}
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleAddVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleAddVertex.java
index 9ebdcb2..7b4bfd1 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleAddVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleAddVertex.java
@@ -5,8 +5,8 @@
import edu.uci.ics.genomix.type.EdgeListWritable;
import edu.uci.ics.genomix.type.EdgeWritable;
-import edu.uci.ics.genomix.type.NodeWritable.DirectionFlag;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
+import edu.uci.ics.genomix.type.NodeWritable.DirectionFlag;
import edu.uci.ics.pregelix.api.graph.Vertex;
import edu.uci.ics.pregelix.api.job.PregelixJob;
@@ -16,6 +16,7 @@
import edu.uci.ics.genomix.pregelix.format.InitialGraphCleanInputFormat;
import edu.uci.ics.genomix.pregelix.io.MessageWritable;
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
+import edu.uci.ics.genomix.pregelix.type.MessageFlag;
/*
* vertexId: BytesWritable
@@ -53,10 +54,14 @@
public static final String KMER_SIZE = "BasicGraphCleanVertex.kmerSize";
public static int kmerSize = -1;
- private VKmerBytesWritable majorVertexId = new VKmerBytesWritable("ATA"); //forward
- private VKmerBytesWritable middleVertexId = new VKmerBytesWritable("CTA"); //reverse
- private VKmerBytesWritable minorVertexId = new VKmerBytesWritable("AGA"); //forward
- private VKmerBytesWritable insertedBubble = new VKmerBytesWritable("GTA"); //reverse
+ private VKmerBytesWritable majorVertexId = new VKmerBytesWritable("ACA"); //forward
+ private VKmerBytesWritable middleVertexId = new VKmerBytesWritable("ATG"); //reverse
+ private VKmerBytesWritable minorVertexId = new VKmerBytesWritable("TCA"); //forward
+ private VKmerBytesWritable insertedBubble = new VKmerBytesWritable("ATT"); //reverse
+ private byte majorToNewBubbleDir = MessageFlag.DIR_RR;
+ private byte minorToNewBubbleDir = MessageFlag.DIR_FR;
+
+ private EdgeListWritable[] edges = new EdgeListWritable[4];
/**
* initiate kmerSize, length
@@ -99,21 +104,32 @@
getVertexValue().getEdgeList(dir).add(newEdge);
}
+ public void setupEdgeForInsertedBubble(){
+ for (byte d : DirectionFlag.values) {
+ edges[d] = new EdgeListWritable();
+ }
+ edges[majorToNewBubbleDir].add(majorVertexId);
+ edges[minorToNewBubbleDir].add(minorVertexId);
+ }
+
@Override
public void compute(Iterator<MessageWritable> msgIterator) {
initVertex();
if(getSuperstep() == 1){
if(getVertexId().equals(majorVertexId)){
/** add edge pointing to insertedBubble **/
- addEdgeToInsertedBubble(DirectionFlag.DIR_FR, insertedBubble);
+ addEdgeToInsertedBubble(majorToNewBubbleDir, insertedBubble);
}
else if(getVertexId().equals(minorVertexId)){
/** add edge pointing to insertedBubble **/
- addEdgeToInsertedBubble(DirectionFlag.DIR_RF, insertedBubble);
+ addEdgeToInsertedBubble(minorToNewBubbleDir, insertedBubble);
}
else if(getVertexId().equals(middleVertexId)){
+ /** setup edges of insertedBubble**/
+ setupEdgeForInsertedBubble();
+
/** insert new bubble **/
- insertBubble(getVertexValue().getEdges(), insertedBubble, getVertexValue().getInternalKmer());
+ insertBubble(edges, insertedBubble, getVertexValue().getInternalKmer());
}
}
voteToHalt();
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
index ee6efc1..e1ecb0c 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
@@ -14,7 +14,6 @@
import edu.uci.ics.genomix.pregelix.format.GraphCleanInputFormat;
import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
import edu.uci.ics.genomix.pregelix.io.BubbleMergeMessageWritable;
-import edu.uci.ics.genomix.pregelix.io.BubbleMergeMessageWritable.DirToMajor;
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
import edu.uci.ics.genomix.pregelix.operator.BasicGraphCleanVertex;
import edu.uci.ics.genomix.pregelix.type.MessageFlag;
@@ -28,8 +27,15 @@
public static final String DISSIMILARITY_THRESHOLD = "BubbleMergeVertex.dissimilarThreshold";
private float dissimilarThreshold = -1;
+ public static class EdgeType{
+ public static final byte INCOMINGEDGE = 0b1 << 0;
+ public static final byte OUTGOINGEDGE = 0b1 << 1;
+ }
+
private Map<VKmerBytesWritable, ArrayList<BubbleMergeMessageWritable>> receivedMsgMap = new HashMap<VKmerBytesWritable, ArrayList<BubbleMergeMessageWritable>>();
private ArrayList<BubbleMergeMessageWritable> receivedMsgList = new ArrayList<BubbleMergeMessageWritable>();
+ private BubbleMergeMessageWritable topCoverageMessage = new BubbleMergeMessageWritable();
+ private BubbleMergeMessageWritable curMessage = new BubbleMergeMessageWritable();
private Set<BubbleMergeMessageWritable> unchangedSet = new HashSet<BubbleMergeMessageWritable>();
private Set<BubbleMergeMessageWritable> deletedSet = new HashSet<BubbleMergeMessageWritable>();
@@ -60,35 +66,38 @@
}
public void sendBubbleAndMajorVertexMsgToMinorVertex(){
- /** get majorVertex and minorVertex and meToMajorDir**/
+ /** get majorVertex and minorVertex and meToMajorDir and meToMinorDir **/
byte incomingEdgeToMeDir = 0;
if(!getVertexValue().getEdgeList(MessageFlag.DIR_RR).isEmpty()){
incomingEdge.setAsCopy(getVertexValue().getEdgeList(MessageFlag.DIR_RR).get(0).getKey());
- incomingEdgeToMeDir = DirToMajor.FORWARD;
+ incomingEdgeToMeDir = MessageFlag.DIR_RR;
} else{
incomingEdge.setAsCopy(getVertexValue().getEdgeList(MessageFlag.DIR_RF).get(0).getKey());
- incomingEdgeToMeDir = DirToMajor.REVERSE;
+ incomingEdgeToMeDir = MessageFlag.DIR_RF;
}
byte outgoingEdgeToMeDir = 0;
if(!getVertexValue().getEdgeList(MessageFlag.DIR_FF).isEmpty()){
outgoingEdge.setAsCopy(getVertexValue().getEdgeList(MessageFlag.DIR_FF).get(0).getKey());
- outgoingEdgeToMeDir = DirToMajor.FORWARD;
+ outgoingEdgeToMeDir = MessageFlag.DIR_FF;
} else{
outgoingEdge.setAsCopy(getVertexValue().getEdgeList(MessageFlag.DIR_FR).get(0).getKey());
- outgoingEdgeToMeDir = DirToMajor.REVERSE;
+ outgoingEdgeToMeDir = MessageFlag.DIR_FR;
}
majorVertexId.setAsCopy(incomingEdge.compareTo(outgoingEdge) >= 0 ? incomingEdge : outgoingEdge);
minorVertexId.setAsCopy(incomingEdge.compareTo(outgoingEdge) < 0 ? incomingEdge : outgoingEdge);
byte majorToMeDir = (incomingEdge.compareTo(outgoingEdge) >= 0 ? incomingEdgeToMeDir : outgoingEdgeToMeDir);
byte meToMajorDir = mirrorDirection(majorToMeDir);
+ byte minorToMeDir = (incomingEdge.compareTo(outgoingEdge) < 0 ? incomingEdgeToMeDir : outgoingEdgeToMeDir);
+ byte meToMinorDir = mirrorDirection(minorToMeDir);
/** setup outgoingMsg **/
outgoingMsg.setMajorVertexId(majorVertexId);
outgoingMsg.setSourceVertexId(getVertexId());
outgoingMsg.setNode(getVertexValue().getNode());
outgoingMsg.setMeToMajorDir(meToMajorDir);
+ outgoingMsg.setMeToMinorDir(meToMinorDir);
sendMsg(minorVertexId, outgoingMsg);
}
@@ -110,24 +119,51 @@
}
}
+ public byte getEdgeTypeFromDir(byte dir){
+ switch(dir){
+ case MessageFlag.DIR_FF:
+ case MessageFlag.DIR_FR:
+ return EdgeType.OUTGOINGEDGE;
+ case MessageFlag.DIR_RF:
+ case MessageFlag.DIR_RR:
+ return EdgeType.INCOMINGEDGE;
+ }
+ return 0;
+ }
+
+ public boolean isSameEdgeType(byte edgeDir1, byte edgeDir2){
+ return getEdgeTypeFromDir(edgeDir1) == getEdgeTypeFromDir(edgeDir2);
+ }
+
+ public boolean isValidMajorAndMinor(){
+ byte topBubbleToMajorDir = topCoverageMessage.getMeToMajorDir();
+ byte curBubbleToMajorDir = curMessage.getMeToMajorDir();
+ byte topBubbleToMinorDir = topCoverageMessage.getMeToMinorDir();
+ byte curBubbleToMinorDir = curMessage.getMeToMinorDir();
+ return isSameEdgeType(topBubbleToMajorDir, curBubbleToMajorDir) && isSameEdgeType(topBubbleToMinorDir, curBubbleToMinorDir);
+ }
+
public void processSimilarSetToUnchangeSetAndDeletedSet(){
unchangedSet.clear();
deletedSet.clear();
- BubbleMergeMessageWritable topCoverageMessage = new BubbleMergeMessageWritable();
- BubbleMergeMessageWritable tmpMessage = new BubbleMergeMessageWritable();
+ topCoverageMessage.reset();
+ curMessage.reset();
Iterator<BubbleMergeMessageWritable> it;
while(!receivedMsgList.isEmpty()){
it = receivedMsgList.iterator();
topCoverageMessage.set(it.next());
it.remove(); //delete topCoverage node
while(it.hasNext()){
- tmpMessage.set(it.next());
+ curMessage.set(it.next());
+ //check if the vertex is valid minor and if it comes from valid major
+ if(!isValidMajorAndMinor())
+ continue;
//compute the similarity
- float fracDissimilar = topCoverageMessage.computeDissimilar(tmpMessage);
+ float fracDissimilar = topCoverageMessage.computeDissimilar(curMessage);
if(fracDissimilar < dissimilarThreshold){ //if similar with top node, delete this node and put it in deletedSet
//add coverage to top node
- topCoverageMessage.getNode().mergeCoverage(tmpMessage.getNode());
- deletedSet.add(tmpMessage);
+ topCoverageMessage.getNode().addWithNode(curMessage.getNode());
+ deletedSet.add(curMessage);
it.remove();
}
}
@@ -156,7 +192,7 @@
public void compute(Iterator<BubbleMergeMessageWritable> msgIterator) {
initVertex();
if (getSuperstep() == 1) {
- if(VertexUtil.isPathVertex(getVertexValue())){
+ if(VertexUtil.isBubbleVertex(getVertexValue())){
/** send bubble and major vertex msg to minor vertex **/
sendBubbleAndMajorVertexMsgToMinorVertex();
}
@@ -185,7 +221,7 @@
broadcaseKillself();
} else if(incomingMsg.getFlag() == MessageFlag.UNCHANGE){
/** update average coverage **/
- getVertexValue().setAvgCoverage(incomingMsg.getNode().getAverageCoverage());
+ getVertexValue().setNode(incomingMsg.getNode());
}
}
} else if(getSuperstep() == 4){
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/VertexUtil.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/VertexUtil.java
index 4db034e..e10fa7a 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/VertexUtil.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/util/VertexUtil.java
@@ -153,6 +153,11 @@
return isPathVertex(value) || (value.inDegree() == 1 && !isPathVertex(value));
}
+ /**
+ * check condition for starting to send msg
+ * @param value
+ * @return
+ */
public static boolean isVertexWithOnlyOneIncoming(VertexValueWritable value){
return value.inDegree() == 1 && !isPathVertex(value);
}
@@ -172,4 +177,16 @@
public static boolean isActiveVertex(VertexValueWritable value){
return value.inDegree() == 1 || value.outDegree() == 1;
}
+
+ /**
+ * check if the vertex is bubble
+ */
+ public static boolean isBubbleVertex(VertexValueWritable value){
+ return value.inDegree() > 0 && value.outDegree() > 0;
+ }
+
+ /**
+ * check if the vertex is major or minor
+ */
+
}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleAddTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleAddTestSuite.java
index 9f062af..f830b8e 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleAddTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleAddTestSuite.java
@@ -6,7 +6,7 @@
public static Test suite() throws Exception {
String pattern ="BubbleAdd";
- String testSet[] = {"5"};
+ String testSet[] = {"AdjFR"};
init(pattern, testSet);
BasicGraphCleanTestSuite testSuite = new BasicGraphCleanTestSuite();
return makeTestSuite(testSuite);
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleMergeTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleMergeTestSuite.java
index f0f4b91..af5c312 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleMergeTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleMergeTestSuite.java
@@ -6,7 +6,7 @@
public static Test suite() throws Exception {
String pattern ="BubbleMerge";
- String testSet[] = {"CTA_GTA_FR_RF"};
+ String testSet[] = {"BubbleWithTip"};//, "LtoL", "LtoR", "RtoL", "RtoR"};
init(pattern, testSet);
BasicGraphCleanTestSuite testSuite = new BasicGraphCleanTestSuite();
return makeTestSuite(testSuite);
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeTestSuite.java
index a272e20..502db80 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeTestSuite.java
@@ -20,17 +20,18 @@
// };
String PreFix = "BubbleMerge_Input";
String testSet[] = { PreFix + File.separator
- + "SimpleBubble", PreFix + File.separator
- + "LtoL", PreFix + File.separator
- + "LtoR", PreFix + File.separator
- + "RtoL", PreFix + File.separator
- + "RtoR", PreFix + File.separator
- + "InvalidBubble", PreFix + File.separator
- + "BubbleWithTip", PreFix + File.separator
- + "SideBubble", PreFix + File.separator
- + "OverlapBubble", PreFix + File.separator
- + "Rectangle", PreFix + File.separator
- + "Grid"};
+ + "BubbleWithTip"};
+// , PreFix + File.separator
+// + "LtoL", PreFix + File.separator
+// + "LtoR", PreFix + File.separator
+// + "RtoL", PreFix + File.separator
+// + "RtoR"};//, PreFix + File.separator
+// + "InvalidBubble", PreFix + File.separator
+// + "BubbleWithTip", PreFix + File.separator
+// + "SideBubble", PreFix + File.separator
+// + "OverlapBubble", PreFix + File.separator
+// + "Rectangle", PreFix + File.separator
+// + "Grid"};
init(pattern, testSet);
BasicGraphCleanTestSuite testSuite = new BasicGraphCleanTestSuite();
return makeTestSuite(testSuite);