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Realign existing indels (from the aligner) to leftmost position 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@848 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-05-28 04:56:51 +00:00
parent aa17c4a468
commit 19f9ac2b05
1 changed files with 43 additions and 0 deletions
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43
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java
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@ -171,6 +171,10 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
// decide which reads potentially need to be cleaned
for ( SAMRecord read : reads ) {
// first, move existing indels (for 1 indel reads only) to leftmost position within identical sequence
if ( read.getAlignmentBlocks().size() == 2 )
indelRealignment(read, reference, read.getAlignmentStart()-(int)leftmostIndex);
AlignedRead aRead = new AlignedRead(read);
int mismatchScore = mismatchQualitySum(aRead, reference, read.getAlignmentStart()-(int)leftmostIndex);
@ -407,6 +411,45 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
aRead.getRead().setCigar(readCigar);
}
private void indelRealignment(SAMRecord read, String refSeq, int refIndex) {
Cigar cigar = read.getCigar();
CigarElement ce1 = cigar.getCigarElement(0);
CigarElement ce2 = cigar.getCigarElement(1);
int difference = 0;
if ( ce2.getOperator() == CigarOperator.D ) {
int indelIndex = refIndex + ce1.getLength();
String indelString = refSeq.substring(indelIndex, indelIndex+ce2.getLength());
int newIndex = indelIndex;
while ( newIndex > 0 ) {
String newIndelString = refSeq.substring(newIndex-1, newIndex+ce2.getLength()-1);
if ( !indelString.equals(newIndelString) )
break;
newIndex--;
}
difference = indelIndex - newIndex;
} else if ( ce2.getOperator() == CigarOperator.I ) {
int indelIndex = ce1.getLength();
String indelString = read.getReadString().substring(indelIndex, indelIndex+ce2.getLength());
int newIndex = indelIndex;
while ( newIndex > 0 ) {
String newIndelString = read.getReadString().substring(newIndex-1, newIndex+ce2.getLength()-1);
if ( !indelString.equals(newIndelString) )
break;
newIndex--;
}
difference = indelIndex - newIndex;
}
if ( difference > 0 ) {
Cigar newCigar = new Cigar();
newCigar.add(new CigarElement(ce1.getLength()-difference, CigarOperator.M));
newCigar.add(ce2);
newCigar.add(new CigarElement(cigar.getCigarElement(2).getLength()+difference, CigarOperator.M));
read.setCigar(newCigar);
}
}
private class AlignedRead {
SAMRecord read;
int mismatchScoreToReference;