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ignore clipped reads for realigning indel positions 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1006 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-06-15 01:01:27 +00:00
parent 93dc2cdc70
commit f6af190b74
1 changed files with 6 additions and 3 deletions
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9
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java
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@ -654,7 +654,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
CigarElement ce1 = cigar.getCigarElement(0); CigarElement ce1 = cigar.getCigarElement(0);
CigarElement ce2 = cigar.getCigarElement(1); CigarElement ce2 = cigar.getCigarElement(1);
int difference = 0; // we can move indel 'difference' bases left int difference = 0; // we can move indel 'difference' bases left
final int indel_length = ce2.getLength(); final int indel_length = ce2.getLength();
@ -665,9 +665,12 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
if ( ce2.getOperator() == CigarOperator.D ) if ( ce2.getOperator() == CigarOperator.D )
indelString = refSeq.substring(indelIndexOnRef, indelIndexOnRef+ce2.getLength()).toUpperCase(); // deleted bases indelString = refSeq.substring(indelIndexOnRef, indelIndexOnRef+ce2.getLength()).toUpperCase(); // deleted bases
else if ( ce2.getOperator() == CigarOperator.I ) { else if ( ce2.getOperator() == CigarOperator.I )
indelString = readSeq.substring(indelIndexOnRead, indelIndexOnRead+ce2.getLength()).toUpperCase(); // get the inserted bases indelString = readSeq.substring(indelIndexOnRead, indelIndexOnRead+ce2.getLength()).toUpperCase(); // get the inserted bases
} else
// we can get here if there is soft clipping done at the beginning of the read
// for now, we'll just punt the issue and not try to realign these
return cigar;
// now we have to check all WHOLE periods of the indel sequence: // now we have to check all WHOLE periods of the indel sequence:
// for instance, if // for instance, if