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Trivial code organization for the haplotype score 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4703 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2010-11-18 12:32:55 +00:00
parent 9f356b6cd0
commit 8cba86a69d
1 changed files with 9 additions and 1 deletions
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10
java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
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@ -50,7 +50,15 @@ public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
public boolean useRead(PileupElement p) {
return ! ReadUtils.is454Read(p.getRead());
//return ! (p.getRead() instanceof GATKSAMRecord && ! ((GATKSAMRecord)p.getRead()).isGoodBase(p.getOffset())) && ! ReadUtils.is454Read(p.getRead());
// TODO -- warning, min. mapping quality fixed to constant 1 here for indels. How can I determine the min. mapping quality?
// if ( ReadUtils.is454Read(p.getRead()) ) // we're not a 454 read
// return false;
// else if ( p.getOffset() == -1 ) // indel
// return p.getRead().getMappingQuality() > 0;
// else if ( ! (p.getRead() instanceof GATKSAMRecord) ) // we're not a GATKSamRecord, so we can't filter
// return true;
// else
// return ((GATKSAMRecord)p.getRead()).isGoodBase(p.getOffset()); // we used the base to call the variant
}
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {