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Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Mark DePristo 2011-09-30 08:41:44 -04:00
parent 98ecaf8aa0 cabacf028d
commit d901fed617
2 changed files with 7 additions and 0 deletions
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6
public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
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@ -94,6 +94,12 @@ public class ReadClipper {
if (left == right) if (left == right)
return new SAMRecord(read.getHeader()); return new SAMRecord(read.getHeader());
SAMRecord leftTailRead = hardClipByReferenceCoordinates(right, -1); SAMRecord leftTailRead = hardClipByReferenceCoordinates(right, -1);
// after clipping one tail, it is possible that the consequent hard clipping of adjacent deletions
// make the left cut index no longer part of the read. In that case, clip the read entirely.
if (left > leftTailRead.getAlignmentEnd())
return new SAMRecord(read.getHeader());
ReadClipper clipper = new ReadClipper(leftTailRead); ReadClipper clipper = new ReadClipper(leftTailRead);
return clipper.hardClipByReferenceCoordinatesLeftTail(left); return clipper.hardClipByReferenceCoordinatesLeftTail(left);
} }

1
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
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@ -975,4 +975,5 @@ public class ReadUtils {
AlignmentStartComparator comp = new AlignmentStartComparator(); AlignmentStartComparator comp = new AlignmentStartComparator();
return comp.compare(read1, read2); return comp.compare(read1, read2);
} }
} }