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Merged bug fix from Stable into Unstable

This commit is contained in:
Mauricio Carneiro 2012-08-09 16:09:58 -04:00
parent 58420098ac 67d4148b32
commit abb168e1ba
1 changed files with 9 additions and 2 deletions
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7
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
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@ -261,6 +261,13 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
read.setTemporaryAttribute(GATKSAMRecord.REDUCED_READ_ORIGINAL_ALIGNMENT_START_SHIFT, read.getAlignmentStart()); read.setTemporaryAttribute(GATKSAMRecord.REDUCED_READ_ORIGINAL_ALIGNMENT_START_SHIFT, read.getAlignmentStart());
read.setTemporaryAttribute(GATKSAMRecord.REDUCED_READ_ORIGINAL_ALIGNMENT_END_SHIFT, read.getAlignmentEnd()); read.setTemporaryAttribute(GATKSAMRecord.REDUCED_READ_ORIGINAL_ALIGNMENT_END_SHIFT, read.getAlignmentEnd());
// Check if the read goes beyond the boundaries of the chromosome, and hard clip those boundaries.
int chromosomeLength = ref.getGenomeLocParser().getContigInfo(read.getReferenceName()).getSequenceLength();
if (read.getSoftStart() < 0)
read = ReadClipper.hardClipByReadCoordinates(read, 0, -read.getSoftStart() - 1);
if (read.getSoftEnd() > chromosomeLength)
read = ReadClipper.hardClipByReadCoordinates(read, chromosomeLength - read.getSoftStart() + 1, read.getReadLength() - 1);
if (!DONT_SIMPLIFY_READS) if (!DONT_SIMPLIFY_READS)
read.simplify(); // Clear all unnecessary attributes read.simplify(); // Clear all unnecessary attributes
if (!DONT_CLIP_ADAPTOR_SEQUENCES) if (!DONT_CLIP_ADAPTOR_SEQUENCES)