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Make sure to uppercase ref bases since they aren't coming from the engine 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4364 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2010-09-28 19:05:46 +00:00
parent 37613810bf
commit 7ad87d328d
1 changed files with 1 additions and 0 deletions
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java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -1319,6 +1319,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
long padRight = Math.min(loc.getStop()+REFERENCE_PADDING, referenceReader.getSequenceDictionary().getSequence(loc.getContig()).getSequenceLength());
loc = GenomeLocParser.createGenomeLoc(loc.getContigIndex(), padLeft, padRight);
reference = referenceReader.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getStop()).getBases();
StringUtil.toUpperCase(reference);
}
return reference;