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When remapping the read, set MAPQ, CIGAR etc to 0/null for unmapped reads. This is not required according to spec but current samtools jdk otherwise dies in STRICT validation mode. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5089 348d0f76-0448-11de-a6fe-93d51630548a
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asivache 2011-01-26 19:49:07 +00:00
parent d33162145b
commit 63b709d992
1 changed files with 11 additions and 0 deletions
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11
java/src/org/broadinstitute/sting/playground/utils/GenomicMap.java
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@ -232,6 +232,17 @@ public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeL
// remapped bam
r.setReferenceIndex(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX);
r.setAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
// these are required because current santools jdk is over-validating and requiring MAPQ, CIGAR etc be
// set to 0/null for unmapped reads. In principle, it should not matter.
r.setMappingQuality(0);
r.setCigar(new Cigar());
r.setNotPrimaryAlignmentFlag(false);
if ( r.getReadNegativeStrandFlag() ) {
r.setReadBases(BaseUtils.simpleReverseComplement(r.getReadBases()));
r.setBaseQualities(Utils.reverse(r.getBaseQualities()));
r.setReadNegativeStrandFlag(false);
}
return r; // nothing to do if read is unmapped
}