Updated the CallsetConcordance classes to use new VCF Variation code... and uncovered a whole bunch of VCF bugs in the process. I'm not convinced that I got them all, so I'll unit test like crazy when the refactoring is done.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2272 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java

@@ -259,6 +259,16 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
         return mCurrentRecord.getGenotypes();
     }
 
+    /**
+     * get the genotypes
+     *
+     * @return a list of the genotypes
+     */
+    public List<VCFGenotypeRecord> getVCFGenotypeRecords() {
+        assertNotNull();
+        return mCurrentRecord.getVCFGenotypeRecords();
+    }
+
     /**
      * do we have the specified genotype?  not all backedByGenotypes
      * have all the genotype data.

java/src/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceWalker.java

@@ -130,19 +130,15 @@ public class CallsetConcordanceWalker extends RodWalker<Integer, Integer> {
 
         // pull out all of the individual calls from the rods and insert into a map based on the
         // mapping from rod/sample to uniquified name
-        HashMap<String, VCFGenotypeCall> samplesToRecords = new HashMap<String, VCFGenotypeCall>();
+        HashMap<String, Genotype> samplesToRecords = new HashMap<String, Genotype>();
         for ( RodVCF rod : vcfRods ) {
-            List<Genotype> records = rod.getGenotypes();
+            List<VCFGenotypeRecord> records = rod.getVCFGenotypeRecords();
-            for ( Genotype g : records ) {
+            for ( VCFGenotypeRecord vcfRec : records ) {
-                if ( !(g instanceof VCFGenotypeCall) )
+                String uniquifiedSample = rodNamesToSampleNames.get(new Pair<String, String>(rod.getName(), vcfRec.getSampleName()));
-                    throw new StingException("Expected VCF rod Genotypes to be of type VCFGenotypeCall");
-
-                VCFGenotypeCall vcfCall = (VCFGenotypeCall)g;
-                String uniquifiedSample = rodNamesToSampleNames.get(new Pair<String, String>(rod.getName(), vcfCall.getSampleName()));
                 if ( uniquifiedSample == null )
-                    throw new StingException("Unexpected sample encountered: " + vcfCall.getSampleName() + " in rod " + rod.getName());
+                    throw new StingException("Unexpected sample encountered: " + vcfRec.getSampleName() + " in rod " + rod.getName());
 
-                samplesToRecords.put(uniquifiedSample, vcfCall);
+                samplesToRecords.put(uniquifiedSample, vcfRec);
             }
         }
 
@@ -173,4 +169,4 @@ public class CallsetConcordanceWalker extends RodWalker<Integer, Integer> {
         vcfWriter.close();
         out.printf("Processed %d loci.\n", result);
     }
-}
+}

java/src/org/broadinstitute/sting/gatk/walkers/concordance/ConcordanceType.java

@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.concordance;
 
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeCall;
+import org.broadinstitute.sting.utils.genotype.Genotype;
 
 import java.util.Map;
 import java.util.Set;
@@ -9,6 +9,6 @@ import java.util.Set;
 public interface ConcordanceType {
 
     public void initialize(Map<String,String> args, Set<String> samples);
-    public String computeConcordance(Map<String, VCFGenotypeCall> samplesToRecords, ReferenceContext ref);
+    public String computeConcordance(Map<String, Genotype> samplesToRecords, ReferenceContext ref);
     public String getInfoName();
 }

java/src/org/broadinstitute/sting/gatk/walkers/concordance/IndelSubsets.java

@@ -4,7 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.genotype.Variation;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeCall;
+import org.broadinstitute.sting.utils.genotype.Genotype;
 
 import java.util.*;
 
@@ -53,10 +53,10 @@ public class IndelSubsets implements ConcordanceType {
         }
     }
 
-    public String computeConcordance(Map<String, VCFGenotypeCall> samplesToRecords, ReferenceContext ref) {
+    public String computeConcordance(Map<String, Genotype> samplesToRecords, ReferenceContext ref) {
 
-        VCFGenotypeCall indel1 = samplesToRecords.get(sample1);
+        Genotype indel1 = samplesToRecords.get(sample1);
-        VCFGenotypeCall indel2 = samplesToRecords.get(sample2);
+        Genotype indel2 = samplesToRecords.get(sample2);
 
         int set1 = ( indel1 != null && !indel1.isPointGenotype() ? 0 : 1 );
         int set2 = ( indel2 != null && !indel2.isPointGenotype() ? 0 : 1 );

java/src/org/broadinstitute/sting/gatk/walkers/concordance/NWayVenn.java

@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.concordance;
 
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeCall;
+import org.broadinstitute.sting.utils.genotype.Genotype;
 
 import java.util.*;
 import java.util.Map.Entry;
@@ -18,12 +18,12 @@ public class NWayVenn implements ConcordanceType {
 
     public void initialize(Map<String, String> args, Set<String> samples) { }
 
-    public String computeConcordance(Map<String, VCFGenotypeCall> samplesToRecords, ReferenceContext ref) {
+    public String computeConcordance(Map<String, Genotype> samplesToRecords, ReferenceContext ref) {
         if ( samplesToRecords.size() == 0 )
             return null;
 
         TreeSet<String> concordantSamples = new TreeSet<String>();
-        for ( Entry<String, VCFGenotypeCall> entry : samplesToRecords.entrySet() ) {
+        for ( Entry<String, Genotype> entry : samplesToRecords.entrySet() ) {
             concordantSamples.add(entry.getKey());
         }
 
@@ -39,4 +39,4 @@ public class NWayVenn implements ConcordanceType {
     }
 
     public String getInfoName() { return "NwayVenn"; }    
-}
+}

java/src/org/broadinstitute/sting/gatk/walkers/concordance/SNPGenotypeConcordance.java

@@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.concordance;
 
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeCall;
+import org.broadinstitute.sting.utils.genotype.Genotype;
 
 import java.util.*;
 
@@ -29,10 +29,10 @@ public class SNPGenotypeConcordance implements ConcordanceType {
         sample2 = iter.next();
     }
 
-    public String computeConcordance(Map<String, VCFGenotypeCall> samplesToRecords, ReferenceContext ref) {
+    public String computeConcordance(Map<String, Genotype> samplesToRecords, ReferenceContext ref) {
 
-        VCFGenotypeCall call1 = samplesToRecords.get(sample1);
+        Genotype call1 = samplesToRecords.get(sample1);
-        VCFGenotypeCall call2 = samplesToRecords.get(sample2);
+        Genotype call2 = samplesToRecords.get(sample2);
 
         // the only reason they would be null is a lack of coverage
         if ( call1 == null || call2 == null ) {
@@ -78,9 +78,9 @@ public class SNPGenotypeConcordance implements ConcordanceType {
         }
 
         // one is variant and the other is ref
-        else if ( call1.isPointGenotype() && call2.isVariant() && confidence1 >= Qscore )
+        else if ( call1.isPointGenotype() && call2.isVariant(ref.getBase()) && confidence1 >= Qscore )
              return "set1VariantSet2Ref";
-        else if ( call2.isPointGenotype() && call1.isVariant() && confidence2 >= Qscore )
+        else if ( call2.isPointGenotype() && call1.isVariant(ref.getBase()) && confidence2 >= Qscore )
             return "set1RefSet2Variant";
 
         return null;

java/src/org/broadinstitute/sting/gatk/walkers/concordance/SimpleVenn.java

@@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.concordance;
 
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.genotype.Variation;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeCall;
+import org.broadinstitute.sting.utils.genotype.Genotype;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.util.*;
@@ -25,10 +25,10 @@ public class SimpleVenn implements ConcordanceType {
         sample2 = iter.next();
     }
 
-    public String computeConcordance(Map<String, VCFGenotypeCall> samplesToRecords, ReferenceContext ref) {
+    public String computeConcordance(Map<String, Genotype> samplesToRecords, ReferenceContext ref) {
 
-        VCFGenotypeCall call1 = samplesToRecords.get(sample1);
+        Genotype call1 = samplesToRecords.get(sample1);
-        VCFGenotypeCall call2 = samplesToRecords.get(sample2);
+        Genotype call2 = samplesToRecords.get(sample2);
 
         if ( call1 == null && call2 == null )
             return null;

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeEncoding.java

@@ -25,8 +25,8 @@ public class VCFGenotypeEncoding {
     public VCFGenotypeEncoding(String baseString) {
         if ((baseString.length() == 1)) {
             // are we an empty (no-call) genotype?
-            if (baseString.equals(VCFGenotypeRecord.EMPTY_GENOTYPE)) {
+            if (baseString.equals(VCFGenotypeRecord.EMPTY_ALLELE)) {
-                mBases = VCFGenotypeRecord.EMPTY_GENOTYPE;
+                mBases = VCFGenotypeRecord.EMPTY_ALLELE;
                 mLength = 0;
                 mType = TYPE.UNCALLED;
             } else if (!validBases(baseString)) {
@@ -67,10 +67,14 @@ public class VCFGenotypeEncoding {
     }
 
     public boolean equals(Object obj) {
-        if (obj != null && (obj.getClass().equals(this.getClass()))) {
+        if ( obj == null )
+            return false;
+        if ( obj instanceof VCFGenotypeEncoding ) {
             VCFGenotypeEncoding d = (VCFGenotypeEncoding) obj;
             return (mType == d.mType) && (mBases.equals(d.mBases)) && (mLength == d.mLength);
         }
+        if ( mType == TYPE.UNCALLED && obj.toString().equals(VCFGenotypeRecord.EMPTY_ALLELE) )
+            return true;
         return false;
     }
 
@@ -84,7 +88,7 @@ public class VCFGenotypeEncoding {
     /**
      * dump the string representation of this genotype encoding
      *
-     * @return
+     * @return string representation
      */
     public String toString() {
         StringBuilder builder = new StringBuilder();

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeRecord.java

@@ -16,8 +16,11 @@ import java.util.Map;
  *         <p/>
  */
 public class VCFGenotypeRecord implements Genotype {
-    // the symbol for a empty genotype
+    // the symbols for an empty genotype
-    public static final String EMPTY_GENOTYPE = ".";
+    public static final String EMPTY_GENOTYPE = "./.";
+    public static final String EMPTY_ALLELE = ".";
+
+    public static final int MISSING_DEPTH = -1;
 
     // what kind of phasing this genotype has
     public enum PHASE {
@@ -37,7 +40,7 @@ public class VCFGenotypeRecord implements Genotype {
     private final Map<String, String> mFields = new HashMap<String, String>();
 
     // our sample name
-    private final String mSampleName;
+    private String mSampleName;
 
     /**
      * Create a VCF genotype record
@@ -58,6 +61,10 @@ public class VCFGenotypeRecord implements Genotype {
         this.mRecord = record;
     }
 
+    public void setSampleName(String name) {
+        mSampleName = name;
+    }
+
     /**
      * determine the phase of the genotype
      *
@@ -98,6 +105,15 @@ public class VCFGenotypeRecord implements Genotype {
         return ( mFields.containsKey("GQ") ? Double.valueOf(mFields.get("GQ")) / 10.0 : 0.0);
     }
 
+    public int getReadCount() {
+        int depth = MISSING_DEPTH;
+        if ( mFields.containsKey("RD") )
+            depth = Integer.valueOf(mFields.get("RD"));
+        else if ( mFields.containsKey("DP") )
+            depth = Integer.valueOf(mFields.get("DP"));
+        return depth;
+    }
+
     public GenomeLoc getLocation() {
         return mRecord != null ? mRecord.getLocation() : null;
     }
@@ -157,7 +173,7 @@ public class VCFGenotypeRecord implements Genotype {
         boolean first = true;
         for (VCFGenotypeEncoding allele : mGenotypeAlleles) {
             if (allele.getType() == VCFGenotypeEncoding.TYPE.UNCALLED)
-                str += VCFGenotypeRecord.EMPTY_GENOTYPE;
+                str += VCFGenotypeRecord.EMPTY_ALLELE;
             else
                 str += String.valueOf((altAlleles.contains(allele)) ? altAlleles.indexOf(allele) + 1 : 0);
             if (first) {

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java

@@ -213,8 +213,8 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
 
 
         List<VCFGenotypeEncoding> alleles = new ArrayList<VCFGenotypeEncoding>();
-        alleles.add(new VCFGenotypeEncoding(VCFGenotypeRecord.EMPTY_GENOTYPE));
+        alleles.add(new VCFGenotypeEncoding(VCFGenotypeRecord.EMPTY_ALLELE));
-        alleles.add(new VCFGenotypeEncoding(VCFGenotypeRecord.EMPTY_GENOTYPE));
+        alleles.add(new VCFGenotypeEncoding(VCFGenotypeRecord.EMPTY_ALLELE));
 
         VCFGenotypeRecord record = new VCFGenotypeRecord(sampleName,
                                                          alleles,

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFParameters.java

@@ -65,7 +65,9 @@ class VCFParameters {
     }
 
     public void addAlternateBase(VCFGenotypeEncoding base) {
-        if (!alternateBases.contains(base) && !base.toString().equals(String.valueOf(this.getReferenceBase())))
+        if ( !alternateBases.contains(base) &&
+             !base.toString().equals(String.valueOf(getReferenceBase())) &&
+             !base.toString().equals(VCFGenotypeRecord.EMPTY_ALLELE) )
             alternateBases.add(base);
     }
 

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFReader.java

@@ -206,15 +206,20 @@ public class VCFReader implements Iterator<VCFRecord>, Iterable<VCFRecord> {
         // if we have genotyping data, we try and extract the genotype fields
         if (mHeader.hasGenotypingData()) {
             String mFormatString = tokens[index];
+            String keyStrings[] = mFormatString.split(":");
             List<VCFGenotypeRecord> genotypeRecords = new ArrayList<VCFGenotypeRecord>();
             index++;
 			String[] alt_alleles = values.get(VCFHeader.HEADER_FIELDS.ALT).split(",");
             for (String str : mHeader.getGenotypeSamples()) {
-                if (!tokens[index].equalsIgnoreCase(VCFGenotypeRecord.EMPTY_GENOTYPE))
+                genotypeRecords.add(getVCFGenotype(str, keyStrings, tokens[index], alt_alleles, values.get(VCFHeader.HEADER_FIELDS.REF).charAt(0)));
-                    genotypeRecords.add(getVCFGenotype(str, mFormatString, tokens[index], alt_alleles, values.get(VCFHeader.HEADER_FIELDS.REF).charAt(0)));
                 index++;
             }
-            return new VCFRecord(values, mFormatString, genotypeRecords);
+            VCFRecord vrec = new VCFRecord(values, mFormatString, genotypeRecords);
+            // associate the genotypes with this new record
+            for ( VCFGenotypeRecord gr : genotypeRecords )
+                gr.setVCFRecord(vrec);
+            return vrec;
+
         }
         return new VCFRecord(values);
     }
@@ -231,11 +236,25 @@ public class VCFReader implements Iterator<VCFRecord>, Iterable<VCFRecord> {
      * @return a VCFGenotypeRecord
      */
     public static VCFGenotypeRecord getVCFGenotype(String sampleName, String formatString, String genotypeString, String altAlleles[], char referenceBase) {
+        return getVCFGenotype(sampleName, formatString.split(":"), genotypeString, altAlleles, referenceBase);
+    }
+
+    /**
+     * generate a VCF genotype record, given it's format string, the genotype string, and allele info
+     *
+     * @param sampleName     the sample name
+     * @param keyStrings     the split format string for this record, which contains the keys for the genotype parameters
+     * @param genotypeString contains the phasing information, allele information, and values for genotype parameters
+     * @param altAlleles     the alternate allele string array, which we index into based on the field parameters
+     * @param referenceBase  the reference base
+     *
+     * @return a VCFGenotypeRecord
+     */
+    public static VCFGenotypeRecord getVCFGenotype(String sampleName, String[] keyStrings, String genotypeString, String altAlleles[], char referenceBase) {
         // parameters to create the VCF genotype record
         Map<String, String> tagToValue = new HashMap<String, String>();
         VCFGenotypeRecord.PHASE phase = VCFGenotypeRecord.PHASE.UNKNOWN;
         List<VCFGenotypeEncoding> bases = new ArrayList<VCFGenotypeEncoding>();
-        String keyStrings[] = formatString.split(":");
 
         for (String key : keyStrings) {
             String parse;
@@ -260,11 +279,13 @@ public class VCFReader implements Iterator<VCFRecord>, Iterable<VCFRecord> {
             if (nextDivider + 1 >= genotypeString.length()) nextDivider = genotypeString.length() - 1;
             genotypeString = genotypeString.substring(nextDivider + 1, genotypeString.length());
         }
+        if ( bases.size() > 0 && bases.get(0).equals(VCFGenotypeRecord.EMPTY_ALLELE) )
+            tagToValue.clear();
         // catch some common errors, either there are too many field keys or there are two many field values
-        if (keyStrings.length != tagToValue.size() + ((bases.size() > 0) ? 1 : 0))
+        else if ( keyStrings.length != tagToValue.size() + ((bases.size() > 0) ? 1 : 0))
             throw new RuntimeException("VCFReader: genotype value count doesn't match the key count (expected "
                     + keyStrings.length + " but saw " + tagToValue.size() + ")");
-        else if (genotypeString.length() > 0)
+        else if ( genotypeString.length() > 0 )
             throw new RuntimeException("VCFReader: genotype string contained additional unprocessed fields: " + genotypeString
                     + ".  This most likely means that the format string is shorter then the value fields.");
         return new VCFGenotypeRecord(sampleName, bases, phase, tagToValue);
@@ -280,8 +301,8 @@ public class VCFReader implements Iterator<VCFRecord>, Iterable<VCFRecord> {
      * @param bases         the list of bases for this genotype call
      */
     private static void addAllele(String alleleNumber, String[] altAlleles, char referenceBase, List<VCFGenotypeEncoding> bases) {
-        if (alleleNumber.equals(VCFGenotypeRecord.EMPTY_GENOTYPE)) {
+        if (alleleNumber.equals(VCFGenotypeRecord.EMPTY_ALLELE)) {
-            bases.add(new VCFGenotypeEncoding(VCFGenotypeRecord.EMPTY_GENOTYPE));
+            bases.add(new VCFGenotypeEncoding(VCFGenotypeRecord.EMPTY_ALLELE));
         } else {
             int alleleValue = Integer.valueOf(alleleNumber);
             // check to make sure the allele value is within bounds

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java

@@ -85,11 +85,7 @@ public class VCFRecord implements Variation, VariantBackedByGenotype {
         this.setQual(qual);
         this.setFilterString(filters);
         this.mInfoFields.putAll(infoFields);
-        mGenotypeFormatString = genotypeFormatString;
+        this.mGenotypeFormatString = genotypeFormatString;
-
-        // associate the genotypes with this Variation, then add them
-        for ( VCFGenotypeRecord rec : genotypeObjects )
-            rec.setVCFRecord(this);
         this.mGenotypeFields.addAll(genotypeObjects);
     }
 

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java

@@ -5,8 +5,7 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
 import org.broadinstitute.sting.gatk.refdata.RodVCF;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.Pair;
-import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.genotype.*;
-import org.broadinstitute.sting.utils.genotype.Genotype;
 
 import java.util.*;
 import java.util.Map.Entry;
@@ -116,17 +115,13 @@ public class VCFUtils {
         int freqsSeen = 0;
 
         for ( RodVCF rod : rods ) {
-            List<Genotype> myGenotypes = rod.getGenotypes();
+            List<VCFGenotypeRecord> myGenotypes = rod.getVCFGenotypeRecords();
-            for ( Genotype g : myGenotypes ) {
+            for ( VCFGenotypeRecord call : myGenotypes ) {
-                if ( !(g instanceof VCFGenotypeCall) )
-                    throw new StingException("Expected VCFGenotypeCall object but instead saw " + g.getClass().getSimpleName());
-
                 // set the name to be the new uniquified name and add it to the list of genotypes
-                VCFGenotypeCall call = (VCFGenotypeCall)g;
                 call.setSampleName(rodNamesToSampleNames.get(new Pair<String, String>(rod.getName(), call.getSampleName())));
                 if ( params.getPosition() < 1 )
-                    params.setLocations(call.getLocation(), call.getReference());
+                    params.setLocations(rod.getLocation(), call.getReference());
-                params.addGenotypeRecord(createVCFGenotypeRecord(params, call));
+                params.addGenotypeRecord(createVCFGenotypeRecord(params, call, rod.mCurrentRecord));
                 totalReadDepth += call.getReadCount();
             }
 
@@ -168,6 +163,39 @@ public class VCFUtils {
                 params.getGenotypesRecords());
     }
 
+    /**
+     * create the VCF genotype record
+     *
+     * @param params the VCF parameters object
+     * @param gtype  the genotype
+     * @param vcfrecord  the VCF record
+     *
+     * @return a VCFGenotypeRecord
+     */
+    public static VCFGenotypeRecord createVCFGenotypeRecord(VCFParameters params, VCFGenotypeRecord gtype, VCFRecord vcfrecord) {
+        Map<String, String> map = new HashMap<String, String>();
+
+        // calculate the RMS mapping qualities and the read depth
+        int readDepth = gtype.getReadCount();
+        map.put("RD", String.valueOf(readDepth));
+        params.addFormatItem("RD");
+        double qual = 10.0 * gtype.getNegLog10PError();
+        map.put("GQ", String.format("%.2f", qual));
+        params.addFormatItem("GQ");
+
+        List<VCFGenotypeEncoding> alleles = createAlleleArray(gtype);
+        for (VCFGenotypeEncoding allele : alleles) {
+            params.addAlternateBase(allele);
+        }
+
+        VCFGenotypeRecord record = new VCFGenotypeRecord(gtype.getSampleName(),
+                                                         alleles,
+                                                         VCFGenotypeRecord.PHASE.UNPHASED,
+                                                         map);
+        record.setVCFRecord(vcfrecord);
+        return record;
+    }
+
     /**
      * create the VCF genotype record
      *

java/test/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkewIntegrationTest.java

@@ -61,7 +61,7 @@ public class SecondBaseSkewIntegrationTest extends WalkerTest {
                      + " -R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -A SecondBaseSkew"
                      + " -sample variant -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_pileup_test_chr15.vcf"
                      + " -vcf %s -L chr15:46347148";
-        String expected_md5 = "fe7f6d2b48ecf2c1340b5de98a9d5614";
+        String expected_md5 = "160a8e3826eb745bcfe2f463f73e1ec7";
         WalkerTestSpec spec = new WalkerTestSpec(test_args,1,Arrays.asList(expected_md5));
         executeTest("Testing on locus with many indels", spec);
     }

java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java

@@ -14,7 +14,7 @@ public class CallsetConcordanceIntegrationTest extends WalkerTest {
     public void testSimpleVenn() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B set1,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example1.vcf -B set2,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example2.vcf -CT SimpleVenn", 1,
-                Arrays.asList("2fc12b6f02f4cb589f2fd134e765d6b7"));
+                Arrays.asList("851b68004874f3a2e76d795e7401f8a0"));
         executeTest("testSimpleVenn", spec);
     }
 
@@ -22,7 +22,7 @@ public class CallsetConcordanceIntegrationTest extends WalkerTest {
     public void testSNPConcordance() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B set1,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example1.vcf -B set2,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example2.vcf -CT SNPGenotypeConcordance:qscore=5", 1,
-                Arrays.asList("142bcfcc6bb404cd4bd1a4624fa9a15e"));
+                Arrays.asList("7afb56b30257fe2d66bee7a029d75685"));
         executeTest("testSNPConcordance", spec);
     }
 
@@ -30,7 +30,7 @@ public class CallsetConcordanceIntegrationTest extends WalkerTest {
     public void testNWayVenn() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B set1,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example1.vcf -B set2,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example2.vcf -B set3,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/CEU.sample.vcf -CT NWayVenn", 1,
-                Arrays.asList("9a5910137b6b9745f6e0c3ee711a6bfa"));
+                Arrays.asList("f452c04c600ad10c054f18b0c77b53d5"));
         executeTest("testNWayVenn", spec);
     }
 }