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We found the cause of the inconsistency. Woo hoo! 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5955 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2011-06-07 15:13:58 +00:00
parent ca48ea78df
commit bb6c0db783
1 changed files with 0 additions and 8 deletions
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8
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -1567,14 +1567,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
loc = getToolkit().getGenomeLocParser().createGenomeLoc(loc.getContig(), padLeft, padRight); loc = getToolkit().getGenomeLocParser().createGenomeLoc(loc.getContig(), padLeft, padRight);
reference = referenceReader.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getStop()).getBases(); reference = referenceReader.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getStop()).getBases();
StringUtil.toUpperCase(reference); StringUtil.toUpperCase(reference);
// TODO -- REMOVE ME WHEN WE FIND THE NON-DETERMINISM
if ( OUT_STATS != null ) {
logger.warn("ERIC: padLeft = " + padLeft);
logger.warn("ERIC: padRight = " + padRight);
logger.warn("ERIC: loc = " + loc);
logger.warn("ERIC: reference = " + new String(reference));
}
} }
return reference; return reference;