Removing dependence on extended events for the remaining Variant Annotator modules.

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

@@ -34,6 +34,7 @@ import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@@ -67,18 +68,19 @@ public class AlleleBalance extends InfoFieldAnnotation {
                 continue;
 
             AlignmentContext context = stratifiedContexts.get(genotype.getSampleName());
-            if ( context == null )
+            if ( context == null || !context.hasBasePileup() )
                 continue;
 
-            if ( vc.isSNP() && context.hasBasePileup() ) {
+            final ReadBackedPileup pileup = context.getBasePileup();
-                final String bases = new String(context.getBasePileup().getBases());
+            if ( vc.isSNP() ) {
+                final String bases = new String(pileup.getBases());
                 if ( bases.length() == 0 )
                     return null;
-                char refChr = vc.getReference().toString().charAt(0);
+                final char refChr = vc.getReference().toString().charAt(0);
-                char altChr = vc.getAlternateAllele(0).toString().charAt(0);
+                final char altChr = vc.getAlternateAllele(0).toString().charAt(0);
 
-                int refCount = MathUtils.countOccurrences(refChr, bases);
+                final int refCount = MathUtils.countOccurrences(refChr, bases);
-                int altCount = MathUtils.countOccurrences(altChr, bases);
+                final int altCount = MathUtils.countOccurrences(altChr, bases);
 
                 // sanity check
                 if ( refCount + altCount == 0 )
@@ -87,22 +89,10 @@ public class AlleleBalance extends InfoFieldAnnotation {
                 // weight the allele balance by genotype quality so that e.g. mis-called homs don't affect the ratio too much
                 ratio += genotype.getLog10PError() * ((double)refCount / (double)(refCount + altCount));
                 totalWeights += genotype.getLog10PError();
-            } else if ( vc.isIndel() && context.hasExtendedEventPileup() ) {
-                final ReadBackedExtendedEventPileup indelPileup = context.getExtendedEventPileup();
-                if ( indelPileup == null ) {
-                    continue;
-                }
-                // todo -- actually care about indel length from the pileup (agnostic at the moment)
-                int refCount = indelPileup.getNumberOfElements();
-                int altCount = vc.isSimpleInsertion() ? indelPileup.getNumberOfInsertions() : indelPileup.getNumberOfDeletions();
-
-                if ( refCount + altCount == 0 ) {
-                    continue;
-                }
-
-                ratio += /* todo -- make not uniform */ 1 * ((double) refCount) / (double) (refCount + altCount);
-                totalWeights += 1;
             }
+            // Allele Balance for indels was not being computed correctly (since there was no allele matching).  Instead of
+            // prolonging the life of imperfect code, I've decided to delete it.  If someone else wants to try again from
+            // scratch, be my guest - but make sure it's done correctly!  [EB]
         }
 
         // make sure we had a het genotype

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java

@@ -245,18 +245,10 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
 
         for ( String sample : stratifiedContexts.keySet() ) {
             final AlignmentContext context = stratifiedContexts.get(sample);
-            if ( context == null ) 
+            if ( context == null || !context.hasBasePileup() )
-                continue;
-
-            ReadBackedPileup pileup = null;
-             if (context.hasExtendedEventPileup())
-                 pileup = context.getExtendedEventPileup();
-             else if (context.hasBasePileup())
-                 pileup = context.getBasePileup();
-
-             if (pileup == null)
                 continue;
 
+            final ReadBackedPileup pileup = context.getBasePileup();
             for ( final PileupElement p : pileup ) {
                 if ( p.getRead().isReducedRead() ) // ignore reduced reads
                     continue;

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

@@ -30,14 +30,9 @@ public class MappingQualityZero extends InfoFieldAnnotation implements StandardA
 
         int mq0 = 0;
         for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
-            AlignmentContext context = sample.getValue();
+            final AlignmentContext context = sample.getValue();
-            ReadBackedPileup pileup = null;
+            if ( context.hasBasePileup() ) {
-            if (context.hasExtendedEventPileup())
+                final ReadBackedPileup pileup = context.getBasePileup();
-                pileup = context.getExtendedEventPileup();
-            else if (context.hasBasePileup())
-                pileup = context.getBasePileup();
-
-            if (pileup != null) {
                 for (PileupElement p : pileup ) {
                     if ( p.getMappingQual() == 0 )
                         mq0++;

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java

@@ -53,14 +53,8 @@ public class MappingQualityZeroBySample extends GenotypeAnnotation {
             return null;
 
         int mq0 = 0;
-        ReadBackedPileup pileup = null;
+        if ( context.hasBasePileup() ) {
-        if (vc.isIndel() && context.hasExtendedEventPileup())
+            final ReadBackedPileup pileup = context.getBasePileup();
-            pileup = context.getExtendedEventPileup();
-        else if (context.hasBasePileup())
-            pileup = context.getBasePileup();
-        else return null;
-
-        if (pileup != null) {
             for (PileupElement p : pileup ) {
                 if ( p.getMappingQual() == 0 )
                     mq0++;

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java

@@ -31,13 +31,8 @@ public class MappingQualityZeroFraction extends InfoFieldAnnotation implements E
         for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
             AlignmentContext context = sample.getValue();
             depth += context.size();
-             ReadBackedPileup pileup = null;
+            if ( context.hasBasePileup() ) {
-            if (context.hasExtendedEventPileup())
+                final ReadBackedPileup pileup = context.getBasePileup();
-                pileup = context.getExtendedEventPileup();
-            else if (context.hasBasePileup())
-                pileup = context.getBasePileup();
-
-            if (pileup != null) {
                 for (PileupElement p : pileup ) {
                     if ( p.getMappingQual() == 0 )
                         mq0++;

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java

@@ -45,7 +45,7 @@ public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotati
             if ( context == null )
                 continue;
 
-            depth += context.hasBasePileup() ? context.getBasePileup().depthOfCoverage() : context.getExtendedEventPileup().depthOfCoverage();
+            depth += context.hasBasePileup() ? context.getBasePileup().depthOfCoverage() : 0;
         }
 
         if ( depth == 0 )

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

@@ -39,13 +39,8 @@ public class RMSMappingQuality extends InfoFieldAnnotation implements StandardAn
 
         for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
             AlignmentContext context = sample.getValue();
-            ReadBackedPileup pileup = null;
+            if ( context.hasBasePileup() ) {
-            if (context.hasExtendedEventPileup())
+                final ReadBackedPileup pileup = context.getBasePileup();
-                pileup = context.getExtendedEventPileup();
-            else if (context.hasBasePileup())
-                pileup = context.getBasePileup();
-
-            if (pileup != null) {
                 for (PileupElement p : pileup ) {
                     if ( p.getMappingQual() != QualityUtils.MAPPING_QUALITY_UNAVAILABLE )
                         qualities[index++] = p.getMappingQual();

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java

@@ -1,207 +0,0 @@
-/*
- * Copyright (c) 2010 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.gatk.walkers.annotator;
-
-import org.broadinstitute.sting.commandline.Hidden;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-/**
- * Unsupported
- */
-@Hidden
-public class ReadDepthAndAllelicFractionBySample extends GenotypeAnnotation {
-
-        private static String REF_ALLELE = "REF";
-
-        private static String DEL = "DEL"; // constant, for speed: no need to create a key string for deletion allele every time
-
-        public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref,
-                                            AlignmentContext stratifiedContext, VariantContext vc, Genotype g) {
-            if ( g == null || !g.isCalled() )
-                return null;
-
-            if ( vc.isSNP() )
-                return annotateSNP(stratifiedContext, vc);
-            if ( vc.isIndel() )
-                return annotateIndel(stratifiedContext, vc);
-
-            return null;
-        }
-
-        private Map<String,Object> annotateSNP(AlignmentContext stratifiedContext, VariantContext vc) {
-
-            if ( ! stratifiedContext.hasBasePileup() ) return null;
-
-            HashMap<Byte, Integer> alleleCounts = new HashMap<Byte, Integer>();
-            for ( Allele allele : vc.getAlternateAlleles() )
-                alleleCounts.put(allele.getBases()[0], 0);
-
-            ReadBackedPileup pileup = stratifiedContext.getBasePileup();
-            int totalDepth = pileup.getNumberOfElements();
-
-            Map<String, Object> map = new HashMap<String, Object>();
-            map.put(getKeyNames().get(0), totalDepth); // put total depth in right away
-
-            if ( totalDepth == 0 ) return map; // done, can not compute FA at 0 coverage!!
-
-            int mq0 = 0; // number of "ref" reads that are acually mq0
-            for ( PileupElement p : pileup ) {
-                if ( p.getMappingQual() == 0 ) {
-                    mq0++;
-                    continue;
-                }
-                if ( alleleCounts.containsKey(p.getBase()) ) // non-mq0 read and it's an alt
-                    alleleCounts.put(p.getBase(), alleleCounts.get(p.getBase())+1);
-            }
-
-            if ( mq0 == totalDepth ) return map; // if all reads are mq0, there is nothing left to do
-
-            // we need to add counts in the correct order
-            String[] fracs = new String[alleleCounts.size()];
-            for (int i = 0; i < vc.getAlternateAlleles().size(); i++) {
-                fracs[i] = String.format("%.3f", ((float)alleleCounts.get(vc.getAlternateAllele(i).getBases()[0]))/(totalDepth-mq0));
-            }
-
-            map.put(getKeyNames().get(1), fracs);
-            return map;
-        }
-
-        private Map<String,Object> annotateIndel(AlignmentContext
-            stratifiedContext, VariantContext
-            vc) {
-
-            if ( ! stratifiedContext.hasExtendedEventPileup() ) {
-                return null;
-            }
-
-            ReadBackedExtendedEventPileup pileup = stratifiedContext.getExtendedEventPileup();
-            if ( pileup == null )
-                return null;
-            int totalDepth = pileup.getNumberOfElements();
-
-            Map<String, Object> map = new HashMap<String, Object>();
-            map.put(getKeyNames().get(0), totalDepth); // put total depth in right away
-
-            if ( totalDepth == 0 ) return map;
-            int mq0 = 0; // number of "ref" reads that are acually mq0
-
-            HashMap<String, Integer> alleleCounts = new HashMap<String, Integer>();
-            Allele refAllele = vc.getReference();
-
-            for ( Allele allele : vc.getAlternateAlleles() ) {
-
-                if ( allele.isNoCall() ) {
-                    continue; // this does not look so good, should we die???
-                }
-
-                alleleCounts.put(getAlleleRepresentation(allele), 0);
-            }
-
-            for ( ExtendedEventPileupElement e : pileup.toExtendedIterable() ) {
-
-                if ( e.getMappingQual() == 0 ) {
-                    mq0++;
-                    continue;
-                }
-
-                if ( e.isInsertion() ) {
-
-                    final String b =  e.getEventBases();
-                    if ( alleleCounts.containsKey(b) ) {
-                        alleleCounts.put(b, alleleCounts.get(b)+1);
-                    }
-
-                } else {
-                    if ( e.isDeletion() ) {
-                        if ( e.getEventLength() == refAllele.length() ) {
-                            // this is indeed the deletion allele recorded in VC
-                            final String b = DEL;
-                            if ( alleleCounts.containsKey(b) ) {
-                                alleleCounts.put(b, alleleCounts.get(b)+1);
-                            }
-                        }
-//                    else {
-//                        System.out.print("   deletion of WRONG length found");
-//                    }
-                    }
-                }
-            }
-
-            if ( mq0 == totalDepth ) return map;
-
-            String[] fracs = new String[alleleCounts.size()];
-            for (int i = 0; i < vc.getAlternateAlleles().size(); i++)
-                fracs[i] = String.format("%.3f",
-                        ((float)alleleCounts.get(getAlleleRepresentation(vc.getAlternateAllele(i))))/(totalDepth-mq0));
-
-            map.put(getKeyNames().get(1), fracs);
-
-            //map.put(getKeyNames().get(0), counts);
-            return map;
-        }
-
-        private String getAlleleRepresentation(Allele allele) {
-            if ( allele.isNull() ) { // deletion wrt the ref
-                 return DEL;
-            } else { // insertion, pass actual bases
-                return allele.getBaseString();
-            }
-
-        }
-
-     //   public String getIndelBases()
-        public List<String> getKeyNames() { return Arrays.asList("DP","FA"); }
-
-        public List<VCFFormatHeaderLine> getDescriptions() {
-            return Arrays.asList(new VCFFormatHeaderLine(getKeyNames().get(0),
-                            1,
-                            VCFHeaderLineType.Integer,
-                            "Total read depth per sample, including MQ0"),
-                            new VCFFormatHeaderLine(getKeyNames().get(1),
-                            VCFHeaderLineCount.UNBOUNDED,
-                            VCFHeaderLineType.Float,
-                            "Fractions of reads (excluding MQ0 from both ref and alt) supporting each reported alternative allele, per sample"));
-        }
-}

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

@@ -35,13 +35,8 @@ public class SpanningDeletions extends InfoFieldAnnotation implements StandardAn
         int depth = 0;
         for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
             AlignmentContext context = sample.getValue();
-            ReadBackedPileup pileup = null;
+            if ( context.hasBasePileup() ) {
-            if (context.hasExtendedEventPileup())
+                final ReadBackedPileup pileup = context.getBasePileup();
-                pileup = context.getExtendedEventPileup();
-            else if (context.hasBasePileup())
-                pileup = context.getBasePileup();
-
-            if (pileup != null) {
                 deletions += pileup.getNumberOfDeletions();
                 depth += pileup.getNumberOfElements();
             }

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java

@@ -39,14 +39,8 @@ public class TechnologyComposition extends InfoFieldAnnotation implements Experi
 
         for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
             AlignmentContext context = sample.getValue();
-
+            if ( context.hasBasePileup() ) {
-            ReadBackedPileup pileup = null;
+                final ReadBackedPileup pileup = context.getBasePileup();
-            if (context.hasExtendedEventPileup())
-                pileup = context.getExtendedEventPileup();
-            else if (context.hasBasePileup())
-                pileup = context.getBasePileup();
-
-            if (pileup != null) {
                 for ( PileupElement p : pileup ) {
                     if(ReadUtils.is454Read(p.getRead()))
                         reads454++;

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

@@ -304,12 +304,8 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
         // if the reference base is not ambiguous, we can annotate
         Map<String, AlignmentContext> stratifiedContexts;
         if ( BaseUtils.simpleBaseToBaseIndex(ref.getBase()) != -1 ) {
-            if ( ! context.hasExtendedEventPileup() ) {
+            if ( context.hasBasePileup() ) {
                 stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(context.getBasePileup());
-            } else {
-                stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(context.getExtendedEventPileup());
-            }
-            if ( stratifiedContexts != null ) {
                 annotatedVCs = new ArrayList<VariantContext>(VCs.size());
                 for ( VariantContext vc : VCs )
                     annotatedVCs.add(engine.annotateContext(tracker, ref, stratifiedContexts, vc));