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fixed error in RealignmentEngine due to inclusive vs exclusive ends #6404

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Jan 21, 2020
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fixed error in RealignmentEngine due to inclusive vs exclusive ends #6404

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5 changes: 4 additions & 1 deletion ...java/org/broadinstitute/hellbender/tools/walkers/realignmentfilter/RealignmentEngine.java
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Original file line number Diff line number Diff line change
Expand Up @@ -132,8 +132,11 @@ public static List<List<BwaMemAlignment>> findJointAlignments(List<List<BwaMemAl
return new ArrayList<>(commonAlignments);
}

// note the conversion from exclusive end (BWAMemAlignment) to inclusive end (SimpleInterval) (subtract 1 from the end)
// combined with the conversion from 0-based to 1-based contigs (add 1 to start and end)
// which has the net result of adding 1 to the start and leaving the end alone
private static SimpleInterval convertToInterval(final BwaMemAlignment alignment) {
return new SimpleInterval(Integer.toString(alignment.getRefId()), alignment.getRefStart(), alignment.getRefEnd());
return new SimpleInterval(Integer.toString(alignment.getRefId()), alignment.getRefStart() + 1, alignment.getRefEnd());
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@davidbenjamin Are we sure that the contig is correct? I think alignment.getRefId() is likely to be 0 indexed, which means that you'll start with contig 0 when you want contig 1. And obviously it doesn't work for non-numbered contigs. I think what you need to be doing here is looking it up from bwaMemIndex.getReferenceContigNames().

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Oh. I see, it's using the same method to generate the overlap detectors, so that's ok.

}

private static Strand getStrand(final BwaMemAlignment alignment) {
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