changes to VCF output, and updated MD5's in the integration tests

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1836 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -59,7 +59,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
     @Override
     public String toString() {
         if (this.mCurrentRecord != null)
-            return this.mCurrentRecord.toString();
+            return this.mCurrentRecord.toStringRepresentation(mReader.getHeader());
         else
             return "";
     }

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

@@ -1,7 +1,5 @@
 package org.broadinstitute.sting.utils.genotype.vcf;
 
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.genotype.*;
 
 import java.io.File;
@@ -119,51 +117,35 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
             lazyInitialize(genotypes, mFile, mStream);
 
 
-        VCFParamters params = new VCFParamters();
+        VCFParameters params = new VCFParameters();
         params.addFormatItem("GT");
 
         for (Genotype gtype : genotypes) {
             // setup the parameters
             params.setLocations(gtype.getLocation(), gtype.getReference());
 
-            Map<String, String> map = new HashMap<String, String>();
+            VCFGenotypeRecord record = createVCFGenotypeRecord(params, gtype);
-            if (!(gtype instanceof SampleBacked)) {
-                throw new IllegalArgumentException("Genotypes passed to VCF must be backed by SampledBacked interface");
-            }
-
-            // calculate the RMS mapping qualities and the read depth
-            if (gtype instanceof ReadBacked) {
-                int readDepth = ((ReadBacked) gtype).getReadCount();
-                map.put("RD", String.valueOf(readDepth));
-                params.addFormatItem("RD");
-            }
-            double qual = gtype.getNegLog10PError();
-            map.put("GQ", String.format("%.2f", qual));
-            params.addFormatItem("GQ");
-
-            List<String> alleles = new ArrayList<String>();
-            for (char allele : gtype.getBases().toCharArray()) {
-                alleles.add(String.valueOf(allele));
-                params.addAlternateBase(allele);
-            }
-
-            // TODO -- use the GenotypeMetaData object if it's not null            
-
-            VCFGenotypeRecord record = new VCFGenotypeRecord(((SampleBacked) gtype).getSampleName(),
-                                                             alleles,
-                                                             VCFGenotypeRecord.PHASE.UNPHASED,
-                                                             map);
             params.addGenotypeRecord(record);
         }
 
-        Map<String, String> infoFields = new HashMap<String, String>();
+        Map<String, String> infoFields = getInfoFields(metadata, params);
+
+        double qual = (metadata == null) ? 0 : (metadata.getLOD()) * 10;
+
+        /**
+         * TODO: Eric fix the next line when our LOD scores are 0->Inf based instead
+         * of -3 to Inf based.
+         */
+        if (qual < 0.0) {
+            qual = 0.0;
+        }
 
         VCFRecord vcfRecord = new VCFRecord(params.getReferenceBase(),
                                             params.getContig(),
                                             params.getPosition(),
                                             ".",
                                             params.getAlternateBases(),
-                                            0, /* BETTER VALUE HERE */
+                                            qual,
                                             ".",
                                             infoFields,
                                             params.getFormatString(),
@@ -172,85 +154,79 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
         mWriter.addRecord(vcfRecord);
     }
 
+    /**
+     * get the information fields of the VCF record, given the meta data and parameters
+     *
+     * @param metadata the metadata associated with this multi sample call
+     * @param params   the parameters
+     *
+     * @return a mapping of info field to value
+     */
+    private Map<String, String> getInfoFields(GenotypeMetaData metadata, VCFParameters params) {
+        Map<String, String> infoFields = new HashMap<String, String>();
+        if (metadata != null) {
+            infoFields.put("SB", String.format("%.2f", metadata.getSLOD()));
+            infoFields.put("AF", String.format("%.2f", metadata.getAlleleFrequency()));
+        }
+        infoFields.put("NS", String.valueOf(params.getGenotypesRecords().size()));
+        return infoFields;
+    }
+
+    /**
+     * create the VCF genotype record
+     *
+     * @param params the VCF parameters object
+     * @param gtype  the genotype
+     *
+     * @return a VCFGenotypeRecord
+     */
+    private VCFGenotypeRecord createVCFGenotypeRecord(VCFParameters params, Genotype gtype) {
+        Map<String, String> map = new HashMap<String, String>();
+        if (!(gtype instanceof SampleBacked)) {
+            throw new IllegalArgumentException("Genotypes passed to VCF must be backed by SampledBacked interface");
+        }
+
+        // calculate the RMS mapping qualities and the read depth
+        if (gtype instanceof ReadBacked) {
+            int readDepth = ((ReadBacked) gtype).getReadCount();
+            map.put("RD", String.valueOf(readDepth));
+            params.addFormatItem("RD");
+        }
+        double qual = gtype.getNegLog10PError();
+        map.put("GQ", String.format("%.2f", qual));
+        params.addFormatItem("GQ");
+
+        List<String> alleles = createAlleleArray(gtype);
+        for (String allele : alleles) {
+            params.addAlternateBase(allele);
+        }
+
+        VCFGenotypeRecord record = new VCFGenotypeRecord(((SampleBacked) gtype).getSampleName(),
+                                                         alleles,
+                                                         VCFGenotypeRecord.PHASE.UNPHASED,
+                                                         map);
+        return record;
+    }
+
+    /**
+     * create the allele array?
+     *
+     * @param gtype the gentoype object
+     *
+     * @return a list of string representing the string array of alleles
+     */
+    private List<String> createAlleleArray(Genotype gtype) {
+        List<String> alleles = new ArrayList<String>();
+        for (char allele : gtype.getBases().toCharArray()) {
+            alleles.add(String.valueOf(allele));
+        }
+        return alleles;
+    }
+
     /** @return true if we support multisample, false otherwise */
     @Override
     public boolean supportsMultiSample() {
         return true;
     }
 
-
-    /**
-     * a helper class, which performs a lot of the safety checks on the parameters
-     * we feed to the VCF (like ensuring the same position for each genotype in a call).
-     */
-    class VCFParamters {
-        private char referenceBase = '0';
-        private int position = 0;
-        private String contig = null;
-        private boolean initialized = false;
-        private List<VCFGenotypeRecord> genotypesRecord = new ArrayList<VCFGenotypeRecord>();
-        private List<String> formatList = new ArrayList<String>();
-        private List<String> alternateBases = new ArrayList<String>();
-
-        public void setLocations(GenomeLoc location, char refBase) {
-            // if we haven't set it up, we initialize the object
-            if (!initialized) {
-                initialized = true;
-                this.contig = location.getContig();
-                this.position = (int)location.getStart();
-                if (location.getStart() != location.getStop()) {
-                    throw new IllegalArgumentException("The start and stop locations must be the same");
-                }
-                this.referenceBase = refBase;
-            } else {
-                if (!contig.equals(this.contig))
-                    throw new IllegalArgumentException("The contig name has to be the same at a single locus");
-                if (position != this.position)
-                    throw new IllegalArgumentException("The position has to be the same at a single locus");
-                if (refBase != this.referenceBase)
-                    throw new IllegalArgumentException("The reference base name has to be the same at a single locus");
-            }
-        }
-
-        /** @return get the position */
-        public int getPosition() {
-            return position;
-        }
-
-        /** @return get the contig name */
-        public String getContig() {
-            return contig;
-        }
-
-        /** @return get the reference base */
-        public char getReferenceBase() {
-            return referenceBase;
-        }
-
-        public void addGenotypeRecord(VCFGenotypeRecord record) {
-            this.genotypesRecord.add(record);
-        }
-
-        public void addFormatItem(String item) {
-            if (!formatList.contains(item))
-                formatList.add(item);
-        }
-
-        public void addAlternateBase(char base) {
-            if (!alternateBases.contains(String.valueOf(base)) && base != this.getReferenceBase())
-                alternateBases.add(String.valueOf(base));
-        }
-
-        public List<String> getAlternateBases() {
-            return alternateBases;
-        }
-
-        public String getFormatString() {
-            return Utils.join(";", formatList);
-        }
-
-        public List<VCFGenotypeRecord> getGenotypesRecords() {
-            return genotypesRecord;
-        }
-    }
 }

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

@@ -0,0 +1,83 @@
+package org.broadinstitute.sting.utils.genotype.vcf;
+
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.Utils;
+
+import java.util.List;
+import java.util.ArrayList;
+
+
+/**
+ * a helper class, which performs a lot of the safety checks on the parameters
+ * we feed to the VCF (like ensuring the same position for each genotype in a call).
+ */
+class VCFParameters {
+    private char referenceBase = '0';
+    private int position = 0;
+    private String contig = null;
+    private boolean initialized = false;
+    private List<VCFGenotypeRecord> genotypesRecord = new ArrayList<VCFGenotypeRecord>();
+    private List<String> formatList = new ArrayList<String>();
+    private List<String> alternateBases = new ArrayList<String>();
+
+    public void setLocations(GenomeLoc location, char refBase) {
+        // if we haven't set it up, we initialize the object
+        if (!initialized) {
+            initialized = true;
+            this.contig = location.getContig();
+            this.position = (int) location.getStart();
+            if (location.getStart() != location.getStop()) {
+                throw new IllegalArgumentException("The start and stop locations must be the same");
+            }
+            this.referenceBase = refBase;
+        } else {
+            if (!contig.equals(this.contig))
+                throw new IllegalArgumentException("The contig name has to be the same at a single locus");
+            if (position != this.position)
+                throw new IllegalArgumentException("The position has to be the same at a single locus");
+            if (refBase != this.referenceBase)
+                throw new IllegalArgumentException("The reference base name has to be the same at a single locus");
+        }
+    }
+
+    /** @return get the position */
+    public int getPosition() {
+        return position;
+    }
+
+    /** @return get the contig name */
+    public String getContig() {
+        return contig;
+    }
+
+    /** @return get the reference base */
+    public char getReferenceBase() {
+        return referenceBase;
+    }
+
+    public void addGenotypeRecord(VCFGenotypeRecord record) {
+        this.genotypesRecord.add(record);
+    }
+
+    public void addFormatItem(String item) {
+        if (!formatList.contains(item))
+            formatList.add(item);
+    }
+
+    public void addAlternateBase(String base) {
+        if (!alternateBases.contains(String.valueOf(base)) && base != String.valueOf(this.getReferenceBase()))
+            alternateBases.add(base);
+    }
+
+    public List<String> getAlternateBases() {
+        return alternateBases;
+    }
+
+    public String getFormatString() {
+        return Utils.join(";", formatList);
+    }
+
+    public List<VCFGenotypeRecord> getGenotypesRecords() {
+        return genotypesRecord;
+    }
+}

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

@@ -19,7 +19,7 @@ public class VCFRecord {
     // the alternate bases
     private final List<String> mAlts = new ArrayList<String>();
     // our qual value
-    private int mQual;
+    private double mQual;
     // our filter string
     private String mFilterString;
     // our info fields
@@ -61,7 +61,7 @@ public class VCFRecord {
                      int position,
                      String ID,
                      List<String> altBases,
-                     int qual,
+                     double qual,
                      String filters,
                      Map<String, String> infoFields,
                      String genotypeFormatString,
@@ -117,7 +117,7 @@ public class VCFRecord {
                         addAlternateBase(alt);
                     break;
                 case QUAL:
-                    this.setQual(Integer.valueOf(columnValues.get(val)));
+                    this.setQual(Double.valueOf(columnValues.get(val)));
                     break;
                 case FILTER:
                     this.setFilterString(columnValues.get(val));
@@ -191,7 +191,7 @@ public class VCFRecord {
     }
 
     /** @return the phred-scaled quality score */
-    public int getQual() {
+    public double getQual() {
         return this.mQual;
     }
 
@@ -273,7 +273,7 @@ public class VCFRecord {
         this.mID = mID;
     }
 
-    public void setQual(int mQual) {
+    public void setQual(double mQual) {
         if (mQual < 0)
             throw new IllegalArgumentException("Qual values must be greater than 0");
         this.mQual = mQual;
@@ -307,12 +307,12 @@ public class VCFRecord {
 
     /**
      * the generation of a string representation, which is used by the VCF writer
+     *
      * @return a string
      */
-    public String toString() {
+    public String toStringRepresentation(VCFHeader header) {
         StringBuilder builder = new StringBuilder();
 
-        // else builder.append(FIELD_SEPERATOR + record.getValue(field));
         // CHROM \t POS \t ID \t REF \t ALT \t QUAL \t FILTER \t INFO
         builder.append(getChromosome() + FIELD_SEPERATOR);
         builder.append(getPosition() + FIELD_SEPERATOR);
@@ -321,7 +321,7 @@ public class VCFRecord {
         String alts = "";
         for (String str : this.getAlternateAlleles()) alts += str + ",";
         builder.append((alts.length() > 0) ? alts.substring(0, alts.length() - 1) + FIELD_SEPERATOR : "." + FIELD_SEPERATOR);
-        builder.append(getQual() + FIELD_SEPERATOR);
+        builder.append(String.format("%.2f",getQual()) + FIELD_SEPERATOR);
         builder.append(Utils.join(";", getFilteringCodes()) + FIELD_SEPERATOR);
         String info = "";
         for (String str : this.getInfoValues().keySet()) {
@@ -335,9 +335,30 @@ public class VCFRecord {
         else builder.append(info);
 
         if (this.hasGenotypeData()) {
-            builder.append(FIELD_SEPERATOR + this.getGenotypeFormatString());
+            addGenotypeData(builder, header);
-            for (VCFGenotypeRecord rec : this.getVCFGenotypeRecords()) {
+        }
-                builder.append(FIELD_SEPERATOR);
+        return builder.toString();
+    }
+
+    /**
+     * add the genotype data
+     *
+     * @param builder the string builder
+     * @param header  the header object
+     */
+    private void addGenotypeData(StringBuilder builder, VCFHeader header) {
+        builder.append(FIELD_SEPERATOR + this.getGenotypeFormatString());
+        if (header.getGenotypeSamples().size() < getVCFGenotypeRecords().size())
+            throw new RuntimeException("We have more genotype samples than the header specified");
+
+        Map<String, VCFGenotypeRecord> gMap = genotypeListToMap(getVCFGenotypeRecords());
+
+        for (String genotype : header.getGenotypeSamples()) {
+
+            builder.append(FIELD_SEPERATOR);
+
+            if (gMap.containsKey(genotype)) {
+                VCFGenotypeRecord rec = gMap.get(genotype);
                 if (!rec.toGenotypeString(this.mAlts).equals(""))
                     builder.append(rec.toGenotypeString(this.mAlts));
                 for (String s : rec.getFields().keySet()) {
@@ -345,9 +366,14 @@ public class VCFRecord {
                     builder.append(":");
                     builder.append(rec.getFields().get(s));
                 }
+                gMap.remove(genotype);
+            } else {
+                builder.append(".");
             }
         }
-        return builder.toString();
+        if (gMap.size() != 0) {
+            throw new RuntimeException("We failed to use all the genotype samples; their must be an incosistancy between the header and records");   
+        }
     }
 
     /**
@@ -370,4 +396,19 @@ public class VCFRecord {
         return true;
     }
 
+    /**
+     * create a genotype mapping from a list and their sample names
+     *
+     * @param list a list of genotype samples
+     *
+     * @return a mapping of the sample name to VCF genotype record
+     */
+    private static Map<String, VCFGenotypeRecord> genotypeListToMap(List<VCFGenotypeRecord> list) {
+        Map<String, VCFGenotypeRecord> map = new HashMap<String, VCFGenotypeRecord>();
+        for (VCFGenotypeRecord rec : list) {
+            map.put(rec.getSampleName(), rec);
+        }
+        return map;
+    }
+
 }

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

@@ -1,10 +1,7 @@
 package org.broadinstitute.sting.utils.genotype.vcf;
 
 
-import org.broadinstitute.sting.utils.StingException;
-
 import java.io.*;
-import java.nio.charset.Charset;
 
 /**
  * this class writers VCF files
@@ -75,11 +72,7 @@ public class VCFWriter {
      * @param record the record to output
      */
     public void addRecord(VCFRecord record) {
-        if (record.getColumnCount() != mHeader.getGenotypeSamples().size() + mHeader.getHeaderFields().size()) {
+        String vcfString = record.toStringRepresentation(mHeader);
-            throw new RuntimeException("Record has " + record.getColumnCount() +
-                    " columns, when is should have " + mHeader.getColumnCount());
-        }
-        String vcfString = record.toString();
         try {
             mWriter.write(vcfString + "\n");
         } catch (IOException e) {

java/test/org/broadinstitute/sting/gatk/refdata/RodVCFTest.java

@@ -33,7 +33,7 @@ public class RodVCFTest extends BaseTest {
 
     private static IndexedFastaSequenceFile seq;
     private static File vcfFile = new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample.vcf");
-
+    private VCFHeader mHeader;
     @BeforeClass
     public static void beforeTests() {
         try {
@@ -47,13 +47,13 @@ public class RodVCFTest extends BaseTest {
 
     private RodVCF getVCFObject() {
         RodVCF vcf = new RodVCF("VCF");
-        VCFHeader header = null;
+        mHeader = null;
         try {
-            header = (VCFHeader) vcf.initialize(vcfFile);
+            mHeader = (VCFHeader) vcf.initialize(vcfFile);
         } catch (FileNotFoundException e) {
             fail("Unable to open VCF file");
         }
-        header.checkVCFVersion();
+        mHeader.checkVCFVersion();
         return vcf;
     }
 
@@ -91,7 +91,7 @@ public class RodVCFTest extends BaseTest {
     @Test
     public void testToString() {
         // slightly altered line, due to map ordering
-        String firstLine = "20\t14370\trs6054257\tG\tA\t29\t0\tDP=258;AF=0.786;NS=58\tGT:GQ:DP:HQ\t0|0:48:1:51,51\t1|0:48:8:51,51\t1/1:43:5\n";
+        String firstLine = "20\t14370\trs6054257\tG\tA\t29.00\t0\tDP=258;AF=0.786;NS=58\tGT:GQ:DP:HQ\t0|0:48:1:51,51\t1|0:48:8:51,51\t1/1:43:5\n";
         RodVCF vcf = getVCFObject();
         VCFReader reader = new VCFReader(vcfFile);
         Iterator<RodVCF> iter = vcf.createIterator("VCF", vcfFile);
@@ -99,13 +99,13 @@ public class RodVCFTest extends BaseTest {
         while (iter.hasNext()) {
             VCFRecord rec1 = reader.next();
             VCFRecord rec2 = iter.next().mCurrentRecord;
-            if (!rec1.toString().equals(rec2.toString())) {
+            if (!rec1.toStringRepresentation(mHeader).equals(rec2.toStringRepresentation(mHeader))) {
                 fail("VCF record rec1.toString() != rec2.toString()");
             }
             // verify the first line too
             if (first) {
-                if (!firstLine.equals(rec1.toString() + "\n")) {
+                if (!firstLine.equals(rec1.toStringRepresentation(mHeader) + "\n")) {
-                    fail("VCF record rec1.toString() != expected string :\n" + rec1.toString() + firstLine);
+                    fail("VCF record rec1.toString() != expected string :\n" + rec1.toStringRepresentation(mHeader) + firstLine);
                 }
                 first = false;
             }

java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java

@@ -8,63 +8,63 @@ import java.util.Arrays;
 public class VariantFiltrationIntegrationTest extends WalkerTest {
     @Test
     public void testIntervals() {
-        String[] md5DoC = {"b222d15b300f989dd2a86ff1f500f64b", "21c8e1f9dc65fdfb39347547f9b04011"};
+        String[] md5DoC = {"c0a7e2fc07d565e633b3064f9f3cdaf5", "21c8e1f9dc65fdfb39347547f9b04011"};
         WalkerTestSpec spec1 = new WalkerTestSpec(
                 "-T VariantFiltration -X DepthOfCoverage:max=70 -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-11,000,000 -B variant,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.geli.calls -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -vcf %s -included %s -sample NA12878",
                  2,
                  Arrays.asList(md5DoC));
         executeTest("testDoCFilter", spec1);
 
-        String[] md5AlleleBalance = {"9a59d33b55e5bad0228f2d2d67d4c17d", "a13e4ce6260bf9f33ca99dc808b8e6ad"};
+        String[] md5AlleleBalance = {"aa0f7800cfd346236620ae0eac220817", "a13e4ce6260bf9f33ca99dc808b8e6ad"};
         WalkerTestSpec spec2 = new WalkerTestSpec(
                 "-T VariantFiltration -X AlleleBalance:low=0.25,high=0.75 -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-11,000,000 -B variant,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.geli.calls -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -vcf %s -included %s -sample NA12878",
                  2,
                  Arrays.asList(md5AlleleBalance));
         executeTest("testAlleleBalanceFilter", spec2);
 
-        String[] md5Strand = {"b0a6fb821be2f7b26f8f6d77cbd758a9", "0f7db0aad764268ee8fa3b857df8d87d"};
+        String[] md5Strand = {"9f430f251dbeb58a2f80a1306a5dd492", "0f7db0aad764268ee8fa3b857df8d87d"};
         WalkerTestSpec spec3 = new WalkerTestSpec(
                 "-T VariantFiltration -X FisherStrand:pvalue=0.0001 -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-11,000,000 -B variant,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.geli.calls -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -vcf %s -included %s -sample NA12878",
                  2,
                  Arrays.asList(md5Strand));
         executeTest("testStrandFilter", spec3);
 
-        String[] md5Lod = {"60624843c4c8ae561acc444df565da99", "7e0c4f2b0fda85fd2891eee76c396a55"};
+        String[] md5Lod = {"56177258c0b3944c043f86faee4b42ae", "7e0c4f2b0fda85fd2891eee76c396a55"};
         WalkerTestSpec spec4 = new WalkerTestSpec(
                 "-T VariantFiltration -X LodThreshold:lod=10 -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-11,000,000 -B variant,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.geli.calls -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -vcf %s -included %s -sample NA12878",
                  2,
                  Arrays.asList(md5Lod));
         executeTest("testLodFilter", spec4);
 
-        String[] md5MQ0 = {"5e3d4d6b13e79a5df5171d3e5a9f1bd7", "3203de335621851bccf596242b079e23"};
+        String[] md5MQ0 = {"0e303c32f5c1503f4c875771f28fc46c", "3203de335621851bccf596242b079e23"};
         WalkerTestSpec spec5 = new WalkerTestSpec(
                 "-T VariantFiltration -X MappingQualityZero:max=70 -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-11,000,000 -B variant,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.geli.calls -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -vcf %s -included %s -sample NA12878",
                  2,
                  Arrays.asList(md5MQ0));
         executeTest("testMappingQuality0Filter", spec5);
 
-        String[] md5MQ = {"fdbac9cf332dd45d9c92146157ace65f", "ecc777feedea61f7b570d114c2ab89b1"};
+        String[] md5MQ = {"946462a6199e9453784e0942e18e6830", "ecc777feedea61f7b570d114c2ab89b1"};
         WalkerTestSpec spec6 = new WalkerTestSpec(
                 "-T VariantFiltration -X MappingQuality:min=20 -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-11,000,000 -B variant,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.geli.calls -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -vcf %s -included %s -sample NA12878",
                  2,
                  Arrays.asList(md5MQ));
         executeTest("testRMSMappingQualityFilter", spec6);
 
-        String[] md5OnOff = {"57c5a92bde03adbff9c6ca6eada033c4", "67f2e1bc025833b0fa31f47195198997"};
+        String[] md5OnOff = {"2ff84e104ce73e347e55d272170b4d03", "67f2e1bc025833b0fa31f47195198997"};
         WalkerTestSpec spec7 = new WalkerTestSpec(
                 "-T VariantFiltration -X OnOffGenotypeRatio:threshold=0.9 -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-11,000,000 -B variant,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.geli.calls -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -vcf %s -included %s -sample NA12878",
                  2,
                  Arrays.asList(md5OnOff));
         executeTest("testOnOffGenotypeFilter", spec7);
 
-        String[] md5Clusters = {"44223fa50dac2d9c1096558689cb8493", "8fa6b6ffc93ee7fb8d6b52a7fb7815ef"};
+        String[] md5Clusters = {"e6a1c088678b1c31ff340ebd622b476e", "8fa6b6ffc93ee7fb8d6b52a7fb7815ef"};
         WalkerTestSpec spec8 = new WalkerTestSpec(
                 "-T VariantFiltration -X ClusteredSnps:window=10,snps=3 -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-11,000,000 -B variant,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.geli.calls -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -vcf %s -included %s -sample NA12878",
                  2,
                  Arrays.asList(md5Clusters));
         executeTest("testClusteredSnpsFilter", spec8);
 
-        String[] md5Indels = {"0f03727ac9e6fc43311377b29d12596c", "8e0e915a1cb63d7049e0671ed00101fe"};
+        String[] md5Indels = {"82e555b76c12474154f8e5e402516d73", "8e0e915a1cb63d7049e0671ed00101fe"};
         WalkerTestSpec spec9 = new WalkerTestSpec(
                 "-T VariantFiltration -X IndelArtifact -B indels,PointIndel,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.indels -B cleaned,CleanedOutSNP,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.realigner_badsnps -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-11,000,000 -B variant,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.geli.calls -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -vcf %s -included %s -sample NA12878",
                  2,

java/test/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/VariantsToVCFIntegrationTest.java

@@ -21,7 +21,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
     @Test
     public void testVariantsToVCFUsingGeliInput() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("d1882fd8ecee6a95f561ed3be4d4a435");
+        md5.add("0b96a8046d2a06bd87f57df8bac1678d");
 
         /**
          * the above MD5 was calculated from running the following command:
@@ -50,7 +50,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
     @Test
     public void testGenotypesToVCFUsingGeliInput() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("debeaf31846328eddc0abf226fc72ac0");
+        md5.add("09660faa7cfad8af36602f79461c0605");
 
         /**
          * the above MD5 was calculated from running the following command: