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now the reads that are too long are truly ignored (fix of the fix)

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Andrey Sivachenko 2011-08-17 15:16:23 -04:00
parent 069554efe5
commit 710d34633e
1 changed files with 1 additions and 0 deletions
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1
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
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@ -482,6 +482,7 @@ public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
" Read length="+read.getReadLength()+"; cigar="+read.getCigarString()+"; start="+ " Read length="+read.getReadLength()+"; cigar="+read.getCigarString()+"; start="+
read.getAlignmentStart()+"; end="+read.getAlignmentEnd()+ read.getAlignmentStart()+"; end="+read.getAlignmentEnd()+
"; window start (after trying to accomodate the read)="+normal_context.getStart()+"; window end="+normal_context.getStop()); "; window start (after trying to accomodate the read)="+normal_context.getStart()+"; window end="+normal_context.getStop());
return 1;
} }
} }