Adapt SplitRepeatVertex to new graph structure. TODO: test AdjSplitRepeat
diff --git a/genomix/genomix-pregelix/data/TestSet/SplitRepeat/AdjSplitRepeat/bin/.part-00000.crc b/genomix/genomix-pregelix/data/TestSet/SplitRepeat/AdjSplitRepeat/bin/.part-00000.crc
new file mode 100644
index 0000000..22a96a2
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/SplitRepeat/AdjSplitRepeat/bin/.part-00000.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/SplitRepeat/AdjSplitRepeat/bin/part-00000 b/genomix/genomix-pregelix/data/TestSet/SplitRepeat/AdjSplitRepeat/bin/part-00000
new file mode 100755
index 0000000..7f99bf1
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/SplitRepeat/AdjSplitRepeat/bin/part-00000
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/SplitRepeat/AdjSplitRepeat/graphviz/result.ps b/genomix/genomix-pregelix/data/TestSet/SplitRepeat/AdjSplitRepeat/graphviz/result.ps
new file mode 100644
index 0000000..e52e930
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/SplitRepeat/AdjSplitRepeat/graphviz/result.ps
@@ -0,0 +1,690 @@
+%!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 36 666 270
+%%PageOrientation: Portrait
+0 0 1 beginpage
+gsave
+36 36 630 234 boxprim clip newpath
+1 1 set_scale 0 rotate 40 41 translate
+% GCA
+gsave
+0 0 0.75294 nodecolor
+newpath 0 61 moveto
+0 165 lineto
+56 165 lineto
+56 61 lineto
+closepath fill
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 0 61 moveto
+0 165 lineto
+56 165 lineto
+56 61 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+12.5 148.4 moveto 31 (GCA) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 0 139 moveto
+56 139 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+9.5 122.4 moveto 37 (5':[2]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 0 113 moveto
+56 113 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+8 96.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 0 87 moveto
+56 87 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+16.5 70.4 moveto 23 (1.0) alignedtext
+grestore
+% ATG
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 138 61 moveto
+138 165 lineto
+194 165 lineto
+194 61 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+151 148.4 moveto 30 (ATG) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 138 139 moveto
+194 139 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+152 122.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 138 113 moveto
+194 113 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+146 96.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 138 87 moveto
+194 87 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+154.5 70.4 moveto 23 (1.0) alignedtext
+grestore
+% GCA->ATG
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 56.26 113 moveto
+76.82 113 104.89 113 127.5 113 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 127.78 116.5 moveto
+137.78 113 lineto
+127.78 109.5 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 127.78 116.5 moveto
+137.78 113 lineto
+127.78 109.5 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+74 118.4 moveto 46 (FR: [2]) alignedtext
+grestore
+% ATG->GCA
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 137.51 96.99 moveto
+131.87 94.51 125.87 92.33 120 91 curveto
+100.06 86.48 93.94 86.48 74 91 curveto
+71.34 91.6 68.65 92.38 65.99 93.28 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 64.53 90.09 moveto
+56.49 96.99 lineto
+67.08 96.61 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 64.53 90.09 moveto
+56.49 96.99 lineto
+67.08 96.61 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+74 96.4 moveto 46 (FR: [2]) alignedtext
+grestore
+% ATA
+gsave
+0 0 0.75294 nodecolor
+newpath 276 61 moveto
+276 165 lineto
+332 165 lineto
+332 61 lineto
+closepath fill
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 276 61 moveto
+276 165 lineto
+332 165 lineto
+332 61 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+290 148.4 moveto 28 (ATA) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 276 139 moveto
+332 139 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+285.5 122.4 moveto 37 (5':[3]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 276 113 moveto
+332 113 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+284 96.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 276 87 moveto
+332 87 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+292.5 70.4 moveto 23 (3.0) alignedtext
+grestore
+% ATG->ATA
+gsave
+1 setlinewidth
+0.33333 1 1 edgecolor
+newpath 194.26 113 moveto
+214.82 113 242.89 113 265.5 113 curveto
+stroke
+0.33333 1 1 edgecolor
+newpath 265.78 116.5 moveto
+275.78 113 lineto
+265.78 109.5 lineto
+closepath fill
+1 setlinewidth
+solid
+0.33333 1 1 edgecolor
+newpath 265.78 116.5 moveto
+275.78 113 lineto
+265.78 109.5 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+212 118.4 moveto 46 (RF: [2]) alignedtext
+grestore
+% ATA->ATG
+gsave
+1 setlinewidth
+0.33333 1 1 edgecolor
+newpath 275.83 99.35 moveto
+270.06 97.13 263.93 95.18 258 94 curveto
+237.95 90.02 232.05 90.02 212 94 curveto
+209.31 94.53 206.58 95.23 203.87 96.03 curveto
+stroke
+0.33333 1 1 edgecolor
+newpath 202.5 92.8 moveto
+194.17 99.35 lineto
+204.76 99.42 lineto
+closepath fill
+1 setlinewidth
+solid
+0.33333 1 1 edgecolor
+newpath 202.5 92.8 moveto
+194.17 99.35 lineto
+204.76 99.42 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+212 99.4 moveto 46 (RF: [2]) alignedtext
+grestore
+% CTA
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 428 122 moveto
+428 226 lineto
+484 226 lineto
+484 122 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+442 209.4 moveto 28 (CTA) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 428 200 moveto
+484 200 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+442 183.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 428 174 moveto
+484 174 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+436 157.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 428 148 moveto
+484 148 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+444.5 131.4 moveto 23 (2.0) alignedtext
+grestore
+% ATA->CTA
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 332.04 141.32 moveto
+337.63 145.78 343.73 149.93 350 153 curveto
+371.04 163.31 396.78 168.56 417.63 171.23 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 417.4 174.73 moveto
+427.73 172.38 lineto
+418.19 167.77 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 417.4 174.73 moveto
+427.73 172.38 lineto
+418.19 167.77 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+350 175.4 moveto 60 (FR: [1,3]) alignedtext
+grestore
+% AAT
+gsave
+0 0 0.75294 nodecolor
+newpath 428 0 moveto
+428 104 lineto
+484 104 lineto
+484 0 lineto
+closepath fill
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 428 0 moveto
+428 104 lineto
+484 104 lineto
+484 0 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+441.5 87.4 moveto 29 (AAT) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 428 78 moveto
+484 78 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+437.5 61.4 moveto 37 (5':[1]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 428 52 moveto
+484 52 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+436 35.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 428 26 moveto
+484 26 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+444.5 9.4 moveto 23 (1.0) alignedtext
+grestore
+% ATA->AAT
+gsave
+1 setlinewidth
+0 1 1 edgecolor
+newpath 332.17 101.23 moveto
+338.05 98.81 344.22 96.3 350 94 curveto
+376.53 83.44 383.47 81.56 410 71 curveto
+412.71 69.92 415.5 68.8 418.31 67.66 curveto
+stroke
+0 1 1 edgecolor
+newpath 419.89 70.79 moveto
+427.83 63.77 lineto
+417.25 64.31 lineto
+closepath fill
+1 setlinewidth
+solid
+0 1 1 edgecolor
+newpath 419.89 70.79 moveto
+427.83 63.77 lineto
+417.25 64.31 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+356 99.4 moveto 48 (RR: [1]) alignedtext
+grestore
+% CTA->ATA
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 427.77 142.96 moveto
+422.28 138.35 416.27 134.11 410 131 curveto
+389.11 120.65 363.37 116.12 342.49 114.18 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 342.6 110.68 moveto
+332.37 113.41 lineto
+342.07 117.66 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 342.6 110.68 moveto
+332.37 113.41 lineto
+342.07 117.66 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+350 136.4 moveto 60 (FR: [1,3]) alignedtext
+grestore
+% AGC
+gsave
+1 setlinewidth
+0 0 0 nodecolor
+newpath 566 121 moveto
+566 225 lineto
+622 225 lineto
+622 121 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+578.5 208.4 moveto 31 (AGC) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 566 199 moveto
+622 199 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+580 182.4 moveto 28 (5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 566 173 moveto
+622 173 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+574 156.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+0 0 0 nodecolor
+newpath 566 147 moveto
+622 147 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+582.5 130.4 moveto 23 (1.0) alignedtext
+grestore
+% CTA->AGC
+gsave
+1 setlinewidth
+0.33333 1 1 edgecolor
+newpath 484.26 173.8 moveto
+504.82 173.65 532.89 173.44 555.5 173.28 curveto
+stroke
+0.33333 1 1 edgecolor
+newpath 555.8 176.78 moveto
+565.78 173.2 lineto
+555.75 169.78 lineto
+closepath fill
+1 setlinewidth
+solid
+0.33333 1 1 edgecolor
+newpath 555.8 176.78 moveto
+565.78 173.2 lineto
+555.75 169.78 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+502 179.4 moveto 46 (RF: [3]) alignedtext
+grestore
+% AAT->ATA
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 427.81 44.12 moveto
+405.46 39.47 374.08 36.65 350 49 curveto
+346.23 50.93 342.7 53.33 339.41 56.06 curveto
+stroke
+0 0 0 edgecolor
+newpath 337 53.52 moveto
+332.16 62.94 lineto
+341.82 58.6 lineto
+closepath fill
+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 337 53.52 moveto
+332.16 62.94 lineto
+341.82 58.6 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+357.5 54.4 moveto 45 (FF: [1]) alignedtext
+grestore
+% AGC->CTA
+gsave
+1 setlinewidth
+0.33333 1 1 edgecolor
+newpath 565.95 157.92 moveto
+560.17 155.47 554 153.31 548 152 curveto
+528.02 147.66 521.94 147.48 502 152 curveto
+499.34 152.6 496.65 153.38 493.99 154.28 curveto
+stroke
+0.33333 1 1 edgecolor
+newpath 492.53 151.09 moveto
+484.49 157.99 lineto
+495.08 157.61 lineto
+closepath fill
+1 setlinewidth
+solid
+0.33333 1 1 edgecolor
+newpath 492.53 151.09 moveto
+484.49 157.99 lineto
+495.08 157.61 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+502 157.4 moveto 46 (RF: [3]) alignedtext
+grestore
+endpage
+showpage
+grestore
+%%PageTrailer
+%%EndPage: 1
+%%Trailer
+%%Pages: 1
+%%BoundingBox: 36 36 666 270
+end
+restore
+%%EOF
diff --git a/genomix/genomix-pregelix/data/TestSet/SplitRepeat/AdjSplitRepeat/test.txt b/genomix/genomix-pregelix/data/TestSet/SplitRepeat/AdjSplitRepeat/test.txt
new file mode 100644
index 0000000..717f9ac
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/SplitRepeat/AdjSplitRepeat/test.txt
@@ -0,0 +1,6 @@
+GCA	{[]	[{ATG:[2]}]	[]	[]	{5':[(2-0_0)], ~5':[]}	1.0x}
+ATA	{[]	[{CTA:[1,3]}]	[{ATG:[2]}]	[{AAT:[1]}]	{5':[(3-0_0)], ~5':[]}	3.0x}
+CTA	{[]	[{ATA:[1,3]}]	[{AGC:[3]}]	[]	{5':[], ~5':[]}	2.0x}
+AGC	{[]	[]	[{CTA:[3]}]	[]	{5':[], ~5':[]}	1.0x}
+ATG	{[]	[{GCA:[2]}]	[{ATA:[2]}]	[]	{5':[], ~5':[]}	1.0x}
+AAT	{[{ATA:[1]}]	[]	[]	[]	{5':[(1-0_0)], ~5':[]}	1.0x}