Added back the MQ0 annotation - however, it's not yet standard (since mq0 reads are filtered out by default in the genotyper). But it'll work when using the Annotator as a standalone.

While I'm at it, change getPileup to getBasePileup to remove all of the deprecation warnings.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2502 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java

@@ -39,7 +39,7 @@ public class AlleleBalance extends StandardVariantAnnotation {
             if ( genotypeStr.length() != 2 )
                 return null;
 
-            final String bases = new String(context.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getPileup().getBases()).toUpperCase();
+            final String bases = new String(context.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup().getBases()).toUpperCase();
             if ( bases.length() == 0 )
                 return null;
 

java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java

@@ -14,7 +14,7 @@ public class DepthOfCoverage extends StandardVariantAnnotation {
     public String annotate(ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) {
         int depth = 0;
         for ( String sample : stratifiedContexts.keySet() )
-            depth += stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getPileup().size();
+            depth += stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).size();
         return String.format("%d", depth);
     }
 

java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java

@@ -0,0 +1,30 @@
+package org.broadinstitute.sting.gatk.walkers.annotator;
+
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.genotype.Variation;
+import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
+
+import java.util.Map;
+
+
+public class MappingQualityZero implements VariantAnnotation {
+
+    public String annotate(ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) {
+        int mq0 = 0;
+        for ( String sample : stratifiedContexts.keySet() ) {
+            ReadBackedPileup pileup = stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();
+            for (PileupElement p : pileup ) {
+                if ( p.getMappingQual() == 0 )
+                    mq0++;
+            }
+        }
+        return String.format("%d", mq0);
+    }
+
+    public String getKeyName() { return "MQ0"; }
+
+    public VCFInfoHeaderLine getDescription() { return new VCFInfoHeaderLine(getKeyName(), 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "Total Mapping Quality Zero Reads"); }
+}

java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java

@@ -18,7 +18,7 @@ public class RMSMappingQuality extends StandardVariantAnnotation {
     public String annotate(ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) {
         ArrayList<Integer> qualities = new ArrayList<Integer>();
         for ( String sample : stratifiedContexts.keySet() ) {
-            ReadBackedPileup pileup = stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getPileup();
+            ReadBackedPileup pileup = stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();
             for (PileupElement p : pileup )
                 qualities.add(p.getRead().getMappingQuality());
         }

java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java

@@ -36,7 +36,7 @@ public class RankSumTest implements VariantAnnotation {
                 if ( context == null )
                     continue;
 
-                fillQualsFromPileup(ref.getBase(), variation.getAlternativeBaseForSNP(), context.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getPileup(), refQuals, altQuals);
+                fillQualsFromPileup(ref.getBase(), variation.getAlternativeBaseForSNP(), context.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup(), refQuals, altQuals);
             }
         }
 

java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java

@@ -37,7 +37,7 @@ public class SecondBaseSkew implements VariantAnnotation {
 
         Pair<Integer, Integer> depth = new Pair<Integer, Integer>(0, 0);
         for ( String sample : stratifiedContexts.keySet() ) {
-            Pair<Integer, Integer> sampleDepth = getSecondaryPileupNonrefCount(ref.getBase(), stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getPileup(), snp);
+            Pair<Integer, Integer> sampleDepth = getSecondaryPileupNonrefCount(ref.getBase(), stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup(), snp);
             depth.first += sampleDepth.first;
             depth.second += sampleDepth.second;
         }

java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java

@@ -15,7 +15,7 @@ public class SpanningDeletions extends StandardVariantAnnotation {
         int deletions = 0;
         int depth = 0;
         for ( String sample : stratifiedContexts.keySet() ) {
-            ReadBackedPileup pileup = stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getPileup();
+            ReadBackedPileup pileup = stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();
             deletions += pileup.getNumberOfDeletions();
             depth += pileup.size();
         }

java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java

@@ -166,7 +166,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
         if ( BaseUtils.simpleBaseToBaseIndex(ref.getBase()) != -1 &&
                 variant.isBiallelic() &&
                 variant.isSNP() ) {
-            Map<String, StratifiedAlignmentContext> stratifiedContexts = StratifiedAlignmentContext.splitContextBySample(context.getPileup(), null, null);
+            Map<String, StratifiedAlignmentContext> stratifiedContexts = StratifiedAlignmentContext.splitContextBySample(context.getBasePileup(), null, null);
             if ( stratifiedContexts != null )
                 annotations = getAnnotations(ref, stratifiedContexts, variant, requestedAnnotations);
         }