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Require each filter or feature to declare whether or not they want mapping quality zero reads in the alignment context 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1487 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-08-31 03:37:24 +00:00
parent 1a299dd459
commit 463f80c03e
4 changed files with 5 additions and 3 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFNull.java
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@ -17,4 +17,6 @@ public class IVFNull implements IndependentVariantFeature {
public String getStudyInfo() { public String getStudyInfo() {
return ""; return "";
} }
public boolean useZeroQualityReads() { return false; }
} }

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/RatioFilter.java
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@ -261,7 +261,7 @@ public abstract class RatioFilter implements VariantExclusionCriterion {
rodVariants variant = context.getVariant(); rodVariants variant = context.getVariant();
char ref = context.getReferenceContext().getBase(); char ref = context.getReferenceContext().getBase();
ReadBackedPileup pileup = new ReadBackedPileup(ref, context.getAlignmentContext()); ReadBackedPileup pileup = new ReadBackedPileup(ref, context.getAlignmentContext(useZeroQualityReads()));
if ( applyToVariant(variant) ) { if ( applyToVariant(variant) ) {
Pair<Integer, Integer> counts = scoreVariant(ref, pileup, variant); Pair<Integer, Integer> counts = scoreVariant(ref, pileup, variant);
GenotypeFeatureData gfd = dataTable.get(orderedBases(variant.getBestGenotype())); GenotypeFeatureData gfd = dataTable.get(orderedBases(variant.getBestGenotype()));

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECAlleleBalance.java
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@ -57,7 +57,7 @@ public class VECAlleleBalance implements VariantExclusionCriterion { //extends
char ref = context.getReferenceContext().getBase(); char ref = context.getReferenceContext().getBase();
rodVariants variant = context.getVariant(); rodVariants variant = context.getVariant();
ReadBackedPileup pileup = new ReadBackedPileup(ref, context.getAlignmentContext()); ReadBackedPileup pileup = new ReadBackedPileup(ref, context.getAlignmentContext(useZeroQualityReads()));
Pair<Integer, Integer> counts = scoreVariant(ref, pileup, variant); Pair<Integer, Integer> counts = scoreVariant(ref, pileup, variant);
int n = counts.first + counts.second; int n = counts.first + counts.second;
ratio = counts.first.doubleValue() / (double)n; ratio = counts.first.doubleValue() / (double)n;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantFiltrationWalker.java
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@ -210,7 +210,7 @@ public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
if (VERBOSE) { out.println("Original:\n" + variant); } if (VERBOSE) { out.println("Original:\n" + variant); }
GenomeLoc loc = context.getAlignmentContext().getLocation(); GenomeLoc loc = context.getAlignmentContext(true).getLocation();
paramsWriter.print(loc.getContig() + "\t" + loc.getStart() + "\t"); paramsWriter.print(loc.getContig() + "\t" + loc.getStart() + "\t");
// Apply features that modify the likelihoods and LOD scores // Apply features that modify the likelihoods and LOD scores