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@1486 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/contexts/VariantContext.java

@@ -50,7 +50,6 @@ public class VariantContext {
     public RefMetaDataTracker getTracker() { return tracker; }
     public ReferenceContext getReferenceContext() { return ref; }
     public rodVariants getVariant() { return variant; }
-    public AlignmentContext getAlignmentContext() { return getAlignmentContext(false); }
     public AlignmentContext getAlignmentContext(boolean useMQ0Reads) {
         return (useMQ0Reads ? context : getQ0freeContext());
     }

java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFBinomialStrand.java

@@ -22,8 +22,8 @@ public class IVFBinomialStrand implements IndependentVariantFeature {
         VariantContext context = contextWindow.getContext();
         likelihoods = new double[10];
         
-        ReadBackedPileup pileup = new ReadBackedPileup(context.getReferenceContext().getBase(), context.getAlignmentContext());
-        List<SAMRecord> reads = context.getAlignmentContext().getReads();
+        ReadBackedPileup pileup = new ReadBackedPileup(context.getReferenceContext().getBase(), context.getAlignmentContext(useZeroQualityReads()));
+        List<SAMRecord> reads = context.getAlignmentContext(useZeroQualityReads()).getReads();
         String bases = pileup.getBases();
 
         for (int genotypeIndex = 0; genotypeIndex < Genotype.values().length; genotypeIndex++) {
@@ -59,4 +59,6 @@ public class IVFBinomialStrand implements IndependentVariantFeature {
     public String getStudyInfo() {
         return "";
     }
+
+    public boolean useZeroQualityReads() { return false; }    
 }

java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFPrimaryBases.java

@@ -36,7 +36,7 @@ public class IVFPrimaryBases implements IndependentVariantFeature {
         VariantContext context = contextWindow.getContext();
         likelihoods = new double[10];
 
-        ReadBackedPileup pileup = new ReadBackedPileup(context.getReferenceContext().getBase(), context.getAlignmentContext());
+        ReadBackedPileup pileup = new ReadBackedPileup(context.getReferenceContext().getBase(), context.getAlignmentContext(useZeroQualityReads()));
         String primaryBases = pileup.getBases();
 
         for (int genotypeIndex = 0; genotypeIndex < Genotype.values().length; genotypeIndex++) {
@@ -77,4 +77,6 @@ public class IVFPrimaryBases implements IndependentVariantFeature {
     public String getStudyInfo() {
         return "";
     }
+
+    public boolean useZeroQualityReads() { return false; }    
 }

java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFSecondaryBases.java

@@ -63,7 +63,7 @@ public class IVFSecondaryBases implements IndependentVariantFeature {
         VariantContext context = contextWindow.getContext();
         likelihoods = new double[10];
 
-        ReadBackedPileup pileup = new ReadBackedPileup(context.getReferenceContext().getBase(), context.getAlignmentContext());
+        ReadBackedPileup pileup = new ReadBackedPileup(context.getReferenceContext().getBase(), context.getAlignmentContext(useZeroQualityReads()));
         String primaryBases = pileup.getBases();
         String secondaryBases = pileup.getSecondaryBasePileup();
 
@@ -124,4 +124,6 @@ public class IVFSecondaryBases implements IndependentVariantFeature {
     public String getStudyInfo() {
         return "";
     }
+
+    public boolean useZeroQualityReads() { return false; }
 }

java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IndependentVariantFeature.java

@@ -30,4 +30,6 @@ public interface IndependentVariantFeature {
     public String getStudyHeader();
 
     public String getStudyInfo();
+
+    public boolean useZeroQualityReads();
 }

java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECClusteredSnps.java

@@ -31,8 +31,8 @@ public class VECClusteredSnps implements VariantExclusionCriterion {
             if ( variants[i] == null || variants[i+snpThreshold-1] == null )
                 continue;
 
-            GenomeLoc left = variants[i].getAlignmentContext().getLocation();
-            GenomeLoc right = variants[i+snpThreshold-1].getAlignmentContext().getLocation();
+            GenomeLoc left = variants[i].getAlignmentContext(useZeroQualityReads()).getLocation();
+            GenomeLoc right = variants[i+snpThreshold-1].getAlignmentContext(useZeroQualityReads()).getLocation();
             if ( left.getContigIndex() == right.getContigIndex() ) {
                 distance = Math.abs(right.getStart() - left.getStart());
                 if ( distance <= window ) {

java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECDepthOfCoverage.java

@@ -24,7 +24,7 @@ public class VECDepthOfCoverage implements VariantExclusionCriterion {
 
     public void compute(VariantContextWindow contextWindow) {
         VariantContext context = contextWindow.getContext();
-        depth = context.getAlignmentContext().getReads().size();
+        depth = context.getAlignmentContext(useZeroQualityReads()).getReads().size();
         exclude = depth > maximum;
     }
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECFisherStrand.java

@@ -30,7 +30,7 @@ public class VECFisherStrand implements VariantExclusionCriterion {
         int allele2 = BaseUtils.simpleBaseToBaseIndex(variant.getBestGenotype().charAt(1));
 
         if (allele1 != allele2) {
-            exclude = strandTest(context.getReferenceContext().getBase(), context.getAlignmentContext(), allele1, allele2, pvalueLimit, null);
+            exclude = strandTest(context.getReferenceContext().getBase(), context.getAlignmentContext(useZeroQualityReads()), allele1, allele2, pvalueLimit, null);
         } else {
             exclude = false;
         }

java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECHomopolymer.java

@@ -56,7 +56,7 @@ public class VECHomopolymer implements VariantExclusionCriterion {
 
     public void compute(VariantContextWindow contextWindow) {
         VariantContext context = contextWindow.getContext();
-        AlignmentContext alignmentContext = context.getAlignmentContext();
+        AlignmentContext alignmentContext = context.getAlignmentContext(useZeroQualityReads());
         char[] geno = context.getVariant().getBestGenotype().toCharArray();
         int[] genotype = {-1,-1};
         for (int h = 0; h < 2; h ++) {

java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECMappingQuality.java

@@ -20,7 +20,7 @@ public class VECMappingQuality implements VariantExclusionCriterion {
 
     public void compute(VariantContextWindow contextWindow) {
         VariantContext context = contextWindow.getContext();
-        List<SAMRecord> reads = context.getAlignmentContext().getReads();
+        List<SAMRecord> reads = context.getAlignmentContext(useZeroQualityReads()).getReads();
         int[] qualities = new int[reads.size()];
         for (int i=0; i < reads.size(); i++)
             qualities[i] = reads.get(i).getMappingQuality();

java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECOnOffGenotypeRatio.java

@@ -50,7 +50,7 @@ public class VECOnOffGenotypeRatio implements VariantExclusionCriterion { // ext
         VariantContext context = contextWindow.getContext();
         char ref = context.getReferenceContext().getBase();
 
-        ReadBackedPileup pileup = new ReadBackedPileup(ref, context.getAlignmentContext());
+        ReadBackedPileup pileup = new ReadBackedPileup(ref, context.getAlignmentContext(useZeroQualityReads()));
         Pair<Integer, Integer> counts = scoreVariant(ref, pileup, context.getVariant());
         int n = counts.first + counts.second;
         ratio = counts.first.doubleValue() / (double)n;