Merge branch 'jianfeng/genomix' into jianfeng/genomix-reverse
Conflicts:
genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenMapKmerToRead.java
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapKmerPositionToReadOperator.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapKmerPositionToReadOperator.java
index f625143..8609519 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapKmerPositionToReadOperator.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapKmerPositionToReadOperator.java
@@ -137,8 +137,10 @@
private void appendNodeToBuilder(int tIndex, PositionReference pos, ArrayBackedValueStorage posList2,
ArrayTupleBuilder builder2) {
try {
+ builder2.reset();
builder2.addField(pos.getByteArray(), pos.getStartOffset(), PositionReference.INTBYTES);
builder2.addField(pos.getByteArray(), pos.getStartOffset() + PositionReference.INTBYTES, 1);
+
if (posList2 == null) {
builder2.addFieldEndOffset();
} else {
@@ -163,7 +165,6 @@
throw new IllegalStateException();
}
}
- builder2.reset();
} catch (HyracksDataException e) {
throw new IllegalStateException(
"Failed to Add a field to the tuple by copying the data bytes from a byte array.");
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapReadToNodeOperator.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapReadToNodeOperator.java
index a775d7e..98d21af 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapReadToNodeOperator.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapReadToNodeOperator.java
@@ -247,6 +247,7 @@
return;
}
try {
+ builder.reset();
builder.addField(node.getNodeID().getByteArray(), node.getNodeID().getStartOffset(), node.getNodeID()
.getLength());
builder.getDataOutput().writeInt(node.getCount());
@@ -268,7 +269,6 @@
throw new IllegalStateException("Failed to append tuplebuilder to frame");
}
}
- builder.reset();
} catch (IOException e) {
throw new IllegalStateException("Failed to Add a field to the tupleBuilder.");
}
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenMapKmerToRead.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenMapKmerToRead.java
index 968123e..2872a2d 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenMapKmerToRead.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenMapKmerToRead.java
@@ -76,10 +76,11 @@
tuple.getFieldData(MapKmerPositionToReadOperator.OutputOtherReadIDListField),
tuple.getFieldStart(MapKmerPositionToReadOperator.OutputOtherReadIDListField));
+
String kmerString = "";
if (posInRead > 0) {
if (kmer.getLength() > tuple
- .getFieldLength(ReadsKeyValueParserFactory.OutputKmerField)) {
+ .getFieldLength(MapKmerPositionToReadOperator.OutputKmerField)) {
throw new IllegalArgumentException("Not enough kmer bytes");
}
kmer.setNewReference(