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Fixing PairHMMIndelErrorModel boundary issue 

When checking the limits of a read to clip, it wasn't considering reads that may already been clipped before.
This commit is contained in:
Mauricio Carneiro 2012-07-06 11:48:04 -04:00
parent dd571d9aa0
commit f603d4c48c
1 changed files with 6 additions and 8 deletions
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14
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
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@ -198,21 +198,19 @@ public class PairHMMIndelErrorModel {
} }
} }
else { else {
final int refWindowStart = ref.getWindow().getStart();
final int refWindowStop = ref.getWindow().getStop();
if (DEBUG) { if (DEBUG) {
System.out.format("Read Name:%s, aln start:%d aln stop:%d orig cigar:%s\n",p.getRead().getReadName(), p.getRead().getAlignmentStart(), p.getRead().getAlignmentEnd(), p.getRead().getCigarString()); System.out.format("Read Name:%s, aln start:%d aln stop:%d orig cigar:%s\n",p.getRead().getReadName(), p.getRead().getAlignmentStart(), p.getRead().getAlignmentEnd(), p.getRead().getCigarString());
} }
GATKSAMRecord read = ReadClipper.hardClipAdaptorSequence(p.getRead()); GATKSAMRecord read = ReadClipper.hardClipAdaptorSequence(p.getRead());
if (read.isEmpty()) if (!read.isEmpty() && (read.getSoftEnd() > refWindowStop && read.getSoftStart() < refWindowStop))
continue;
if (read.getSoftEnd() > ref.getWindow().getStop())
read = ReadClipper.hardClipByReferenceCoordinatesRightTail(read, ref.getWindow().getStop()); read = ReadClipper.hardClipByReferenceCoordinatesRightTail(read, ref.getWindow().getStop());
if (read.isEmpty()) if (!read.isEmpty() && (read.getSoftStart() < refWindowStart && read.getSoftEnd() > refWindowStart))
continue;
if (read.getSoftStart() < ref.getWindow().getStart())
read = ReadClipper.hardClipByReferenceCoordinatesLeftTail (read, ref.getWindow().getStart()); read = ReadClipper.hardClipByReferenceCoordinatesLeftTail (read, ref.getWindow().getStart());
if (read.isEmpty()) if (read.isEmpty())