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deal with very large known indels that fall off our ref context 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3745 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-07-08 20:05:16 +00:00
parent 7ff6106c14
commit bd2ba3eb37
1 changed files with 10 additions and 3 deletions
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13
java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
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@ -418,9 +418,7 @@ public class AlignmentUtils {
CigarElement indel = cigar.getCigarElement(indexOfIndel); CigarElement indel = cigar.getCigarElement(indexOfIndel);
int indelLength = indel.getLength(); int indelLength = indel.getLength();
// the indel-based reference string int totalRefBases = 0;
byte[] alt = new byte[refSeq.length + (indelLength * (indel.getOperator() == CigarOperator.D ? -1 : 1))];
for ( int i = 0; i < indexOfIndel; i++ ) { for ( int i = 0; i < indexOfIndel; i++ ) {
CigarElement ce = cigar.getCigarElement(i); CigarElement ce = cigar.getCigarElement(i);
int length = ce.getLength(); int length = ce.getLength();
@ -429,18 +427,27 @@ public class AlignmentUtils {
case M: case M:
readIndex += length; readIndex += length;
refIndex += length; refIndex += length;
totalRefBases += length;
break; break;
case S: case S:
readIndex += length; readIndex += length;
break; break;
case N: case N:
refIndex += length; refIndex += length;
totalRefBases += length;
break; break;
default: default:
break; break;
} }
} }
// sometimes, when there are very large known indels, we won't have enough reference sequence to cover them
if ( totalRefBases + indelLength > refSeq.length )
indelLength -= (totalRefBases + indelLength - refSeq.length);
// the indel-based reference string
byte[] alt = new byte[refSeq.length + (indelLength * (indel.getOperator() == CigarOperator.D ? -1 : 1))];
// add the bases before the indel // add the bases before the indel
System.arraycopy(refSeq, 0, alt, 0, refIndex); System.arraycopy(refSeq, 0, alt, 0, refIndex);
int currentPos = refIndex; int currentPos = refIndex;