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Choose the REF if it scores equal to consensus! 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1145 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-07-01 18:54:27 +00:00
parent 9b182e3063
commit 20fab507a8
1 changed files with 3 additions and 3 deletions
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6
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java
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@ -294,9 +294,9 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
// the mismatch score is the min of its alignment vs. the reference and vs. the alternate // the mismatch score is the min of its alignment vs. the reference and vs. the alternate
int myScore = altAlignment.second; int myScore = altAlignment.second;
if ( myScore > toTest.getMismatchScoreToReference() ) if ( myScore >= toTest.getMismatchScoreToReference() )
myScore = toTest.getMismatchScoreToReference(); myScore = toTest.getMismatchScoreToReference();
// keep track of reads that align better OR EQUAL to the alternate consensus. // keep track of reads that align better to the alternate consensus.
// By pushing alignments with equal scores to the alternate, it means we'll over-call (het -> hom non ref) but are less likely to under-call (het -> ref, het non ref -> het) // By pushing alignments with equal scores to the alternate, it means we'll over-call (het -> hom non ref) but are less likely to under-call (het -> ref, het non ref -> het)
else else
consensus.readIndexes.add(new Pair<Integer, Integer>(j, altAlignment.first)); consensus.readIndexes.add(new Pair<Integer, Integer>(j, altAlignment.first));
@ -384,7 +384,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
} }
} }
// END IF ( improvemenr >= LOD_THRESHOLD ) // END IF ( improvement >= LOD_THRESHOLD )
} else if ( statsOutput != null ) { } else if ( statsOutput != null ) {
try { try {