Merge branch 'master' of github.com:broadinstitute/gsa-unstable

public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java

@@ -34,6 +34,9 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
     private final LinkedList<ActiveRegion> workQueue = new LinkedList<ActiveRegion>();
     private final LinkedHashSet<GATKSAMRecord> myReads = new LinkedHashSet<GATKSAMRecord>();
 
+    // package access for unit testing
+    ActivityProfile profile;
+
     @Override
     public String getTraversalUnits() {
         return "active regions";
@@ -53,7 +56,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
 
         int minStart = Integer.MAX_VALUE;
         final List<ActiveRegion> activeRegions = new LinkedList<ActiveRegion>();
-        ActivityProfile profile = new ActivityProfile(engine.getGenomeLocParser(), walker.hasPresetActiveRegions() );
+        profile = new ActivityProfile(engine.getGenomeLocParser(), walker.hasPresetActiveRegions() );
 
         ReferenceOrderedView referenceOrderedDataView = getReferenceOrderedView(walker, dataProvider, locusView);
 

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

@@ -277,8 +277,12 @@ public class VariantAnnotatorEngine {
             if ( expression.fieldName.equals("ID") ) {
                 if ( vc.hasID() )
                     infoAnnotations.put(expression.fullName, vc.getID());
+            } else if (expression.fieldName.equals("ALT")) {
+                infoAnnotations.put(expression.fullName, vc.getAlternateAllele(0).getDisplayString());
+
             } else if ( vc.hasAttribute(expression.fieldName) ) {
-                infoAnnotations.put(expression.fullName, vc.getAttribute(expression.fieldName));
+                    infoAnnotations.put(expression.fullName, vc.getAttribute(expression.fieldName));
+
             }
         }
     }

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java

@@ -190,6 +190,10 @@ public class UnifiedGenotyperEngine {
                     final VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, null, true, model, perReadAlleleLikelihoodMap);
                     if ( vc != null )
                         results.add(calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model, true, perReadAlleleLikelihoodMap));
+// todo - uncomment if we want to also emit a null ref call (with no QUAL) if there's no evidence for REF and if EMIT_ALL_SITES is set
+//                    else if (UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES)
+//                        results.add(generateEmptyContext(tracker, refContext, null, rawContext));
+
                 }
             }        
         }

public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java

@@ -183,6 +183,10 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
     @Argument(fullName="keepAC0", shortName="keepAC0", doc="If provided, modules that track polymorphic sites will not require that a site have AC > 0 when the input eval has genotypes", required=false)
     private boolean keepSitesWithAC0 = false;
 
+    @Hidden
+    @Argument(fullName="numSamples", shortName="numSamples", doc="If provided, modules that track polymorphic sites will not require that a site have AC > 0 when the input eval has genotypes", required=false)
+    private int numSamplesFromArgument = 0;
+
     /**
      * If true, VariantEval will treat -eval 1 -eval 2 as separate tracks from the same underlying
      * variant set, and evaluate the union of the results.  Useful when you want to do -eval chr1.vcf -eval chr2.vcf etc.
@@ -589,6 +593,14 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
     public boolean isSubsettingToSpecificSamples() { return isSubsettingSamples; }
     public Set<String> getSampleNamesForEvaluation() { return sampleNamesForEvaluation; }
 
+    public int getNumberOfSamplesForEvaluation() {
+        if (sampleNamesForEvaluation!= null &&  !sampleNamesForEvaluation.isEmpty())
+            return sampleNamesForEvaluation.size();
+        else {
+            return numSamplesFromArgument;
+        }
+
+    }
     public Set<String> getSampleNamesForStratification() { return sampleNamesForStratification; }
 
     public List<RodBinding<VariantContext>> getComps() { return comps; }

public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java

@@ -29,7 +29,7 @@ public class AlleleCount extends VariantStratifier {
 
         // There are ploidy x n sample chromosomes
         // TODO -- generalize to handle multiple ploidy
-        nchrom = getVariantEvalWalker().getSampleNamesForEvaluation().size() * getVariantEvalWalker().getSamplePloidy();
+        nchrom = getVariantEvalWalker().getNumberOfSamplesForEvaluation() * getVariantEvalWalker().getSamplePloidy();
         if ( nchrom < 2 )
             throw new UserException.BadArgumentValue("AlleleCount", "AlleleCount stratification requires an eval vcf with at least one sample");
 

public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java

@@ -103,6 +103,11 @@ public class ActivityProfile {
         isActiveList.add(result);
     }
 
+    // for unit testing
+    public List<ActivityProfileResult> getActiveList() {
+        return isActiveList;
+    }
+
     public int size() {
         return isActiveList.size();
     }

public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java

@@ -0,0 +1,126 @@
+package org.broadinstitute.sting.gatk.traversals;
+
+import org.testng.Assert;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMSequenceDictionary;
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider;
+import org.broadinstitute.sting.gatk.datasources.reads.MockLocusShard;
+import org.broadinstitute.sting.gatk.datasources.reads.Shard;
+import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
+import org.broadinstitute.sting.gatk.executive.WindowMaker;
+import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
+import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult;
+import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * Created with IntelliJ IDEA.
+ * User: thibault
+ * Date: 11/13/12
+ * Time: 2:47 PM
+ */
+public class TraverseActiveRegionsTest extends BaseTest {
+
+    private class DummyActiveRegionWalker extends ActiveRegionWalker<Integer, Integer> {
+        private final double prob;
+
+        public DummyActiveRegionWalker() {
+            this.prob = 1.0;
+        }
+
+        @Override
+        public ActivityProfileResult isActive(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+            return new ActivityProfileResult(ref.getLocus(), prob);
+        }
+
+        @Override
+        public Integer map(ActiveRegion activeRegion, RefMetaDataTracker metaDataTracker) {
+            return 0;
+        }
+
+        @Override
+        public Integer reduceInit() {
+            return 0;
+        }
+
+        @Override
+        public Integer reduce(Integer value, Integer sum) {
+            return 0;
+        }
+    }
+
+    private final TraverseActiveRegions<Integer, Integer> t = new TraverseActiveRegions<Integer, Integer>();
+
+    private IndexedFastaSequenceFile reference;
+    private GenomeLocParser genomeLocParser;
+    private ActiveRegionWalker<Integer, Integer> walker;
+
+    @BeforeClass
+    private void init() throws FileNotFoundException {
+        reference = new CachingIndexedFastaSequenceFile(new File(hg19Reference));
+        SAMSequenceDictionary dictionary = reference.getSequenceDictionary();
+        genomeLocParser = new GenomeLocParser(dictionary);
+    }
+
+    @Test
+    public void testAllIntervalsSeen() throws Exception {
+        List<GenomeLoc> intervals = new ArrayList<GenomeLoc>();
+        GenomeLoc interval = genomeLocParser.createGenomeLoc("1", 1, 1);
+        intervals.add(interval);
+
+        LocusShardDataProvider dataProvider = createDataProvider(intervals);
+
+        t.traverse(walker, dataProvider, 0);
+
+        boolean allGenomeLocsSeen = true;
+        for (GenomeLoc loc : intervals) {
+            boolean thisGenomeLocSeen = false;
+            for (ActivityProfileResult active : t.profile.getActiveList()) {
+                if (loc.equals(active.getLoc())) {
+                    thisGenomeLocSeen = true;
+                    break;
+                }
+            }
+            if (!thisGenomeLocSeen) {
+                allGenomeLocsSeen = false;
+                break;
+            }
+        }
+
+        Assert.assertTrue(allGenomeLocsSeen, "Some intervals missing from activity profile");
+    }
+
+    private LocusShardDataProvider createDataProvider(List<GenomeLoc> intervals) {
+        walker = new DummyActiveRegionWalker();
+
+        StingSAMIterator iterator = ArtificialSAMUtils.createReadIterator(new ArrayList<SAMRecord>());
+        Shard shard = new MockLocusShard(genomeLocParser, intervals);
+        WindowMaker windowMaker = new WindowMaker(shard, genomeLocParser,iterator,shard.getGenomeLocs());
+        WindowMaker.WindowMakerIterator window = windowMaker.next();
+
+        GenomeAnalysisEngine engine = new GenomeAnalysisEngine();
+        //engine.setReferenceDataSource(reference);
+        engine.setGenomeLocParser(genomeLocParser);
+        t.initialize(engine);
+
+        return new LocusShardDataProvider(shard, null, genomeLocParser, window.getLocus(), window, reference, new ArrayList<ReferenceOrderedDataSource>());
+    }
+}