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Small bug fix: if a read falls at the edge of an indel event (but is not part of it), don't count it towards consistency computation. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4152 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2010-08-27 20:37:27 +00:00
parent 54355b1864
commit fe19539188
1 changed files with 4 additions and 1 deletions
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5
java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelConsistencyReadCounter.java
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@ -63,9 +63,12 @@ public class IndelConsistencyReadCounter extends ReadWalker<Integer, Integer> {
} }
if ( indel != null ) { if ( indel != null ) {
if ( read.getAlignmentEnd() == indel.getStart() )
return 0;
if ( !containsAnyIndel(read) || !containsIndel(read, indel) ) if ( !containsAnyIndel(read) || !containsIndel(read, indel) )
misalignedReads++; misalignedReads++;
else else
consistentReads++; consistentReads++;
} }