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Bug fix: check to see whether there's a BasePileup before asking for one.

This commit is contained in:
Eric Banks 2012-03-21 12:44:09 -04:00
parent 07c3bd32b3
commit 58245bfa2f
1 changed files with 4 additions and 2 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
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@ -31,8 +31,10 @@ public class LowMQ extends InfoFieldAnnotation {
double total = 0; double total = 0;
for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() )
{ {
ReadBackedPileup pileup = sample.getValue().getBasePileup(); if ( !sample.getValue().hasBasePileup() )
for (PileupElement p : pileup ) continue;
for ( PileupElement p : sample.getValue().getBasePileup() )
{ {
if ( p.getMappingQual() == 0 ) { mq0 += 1; } if ( p.getMappingQual() == 0 ) { mq0 += 1; }
if ( p.getMappingQual() <= 10 ) { mq10 += 1; } if ( p.getMappingQual() <= 10 ) { mq10 += 1; }