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Fixing the issue with reads having insertion immediately followed by a S/H cigar element causing out of window error. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3300 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2010-05-05 15:42:27 +00:00
parent 64640d6b17
commit 0338345bee
1 changed files with 15 additions and 12 deletions
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27
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java
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@ -241,13 +241,17 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
return 0;
}
// if ( read.getAlignmentStart() < normal_context.getStart() ) {
// if ( skippingReads ) return 0; // return if we are legitimately skipping reads over some bad region.
// // this should never happen
// throw new StingException("Read "+read.getReadName()+": out of order on the contig\n"+
// "Read starts at "+read.getReferenceName()+":"+read.getAlignmentStart()+ " (cigar="+read.getCigarString()+
// "); window starts at "+normal_context.getStart());
// }
long alignmentEnd = read.getAlignmentEnd();
Cigar c = read.getCigar();
int lastNonClippedElement = 0; // reverse offset to the last unclipped element
CigarOperator op = null;
// moving backwards from the end of the cigar, skip trailing S or H cigar elements:
do {
lastNonClippedElement++;
op = c.getCigarElement( c.numCigarElements()-lastNonClippedElement ).getOperator();
} while ( op == CigarOperator.H || op == CigarOperator.S );
// now op is the last non-S/H operator in the cigar.
// a little trick here: we want to make sure that current read completely fits into the current
// window so that we can accumulate indel observations over the whole length of the read.
@ -257,9 +261,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
// in this program we assign insertions, internally, to the first base *after* the insertion position.
// Hence, we have to make sure that that extra base is already in the window or we will get IndexOutOfBounds.
long alignmentEnd = read.getAlignmentEnd();
Cigar c = read.getCigar();
if ( c.getCigarElement(c.numCigarElements()-1).getOperator() == CigarOperator.I) alignmentEnd++;
if ( op == CigarOperator.I) alignmentEnd++;
if ( alignmentEnd > normal_context.getStop()) {
@ -1226,8 +1228,9 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
indelsAtSite = indels.get(pos);
} catch (IndexOutOfBoundsException e) {
SAMRecord r = rec.getSAMRecord();
System.out.println("Read "+r.getReadName()+": out of coverage window bounds.Probably window is too small.\n"+
"Read length="+r.getReadLength()+"; cigar="+r.getCigarString()+"; start="+
System.out.println("Failed to add indel observation, probably out of coverage window bounds (trailing indel?):\nRead "+
r.getReadName()+": "+
"read length="+r.getReadLength()+"; cigar="+r.getCigarString()+"; start="+
r.getAlignmentStart()+"; end="+r.getAlignmentEnd()+"; window start="+getStart()+
"; window end="+getStop());
throw e;