Removed the SequenomValidationConvertor and renamed it VariantValidationAssessor since it no longer handles ped/sequenom files (but instead works on vcfs/variantcontexts). Updated all of the wiki docs, including adding instructions on how to convert ped files to vcf, a la Shaun Purcell. We now officially no longer support ped files everyone. Other misc cleanup in the code.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4419 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -1,7 +1,5 @@
 package org.broadinstitute.sting.gatk.refdata;
 
-import edu.mit.broad.picard.genotype.DiploidGenotype;
-import edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods;
 import org.broad.tribble.dbsnp.DbSNPFeature;
 import org.broad.tribble.gelitext.GeliTextFeature;
 import org.broad.tribble.hapmap.HapMapFeature;
@@ -114,15 +112,6 @@ public class VariantContextAdaptors {
         }
     }
 
-
-
-    private static Allele deletionAllele(ReferenceContext ref, int start, int len) {
-        byte[] deletion = new byte[len];
-        System.arraycopy(ref.getBases(), start, deletion, 0, len);
-        return Allele.create(deletion, true);
-    }
-
-
     public static VCFHeader createVCFHeader(Set<VCFHeaderLine> hInfo, VariantContext vc) {
         HashSet<String> names = new LinkedHashSet<String>();
         for ( Genotype g : vc.getGenotypesSortedByName() ) {

java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java

@@ -28,7 +28,6 @@ package org.broadinstitute.sting.gatk.walkers.filters;
 import org.broad.tribble.util.variantcontext.Genotype;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broad.tribble.vcf.*;
-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.contexts.variantcontext.VariantContextUtils;
@@ -37,7 +36,6 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.CommandLineUtils;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;

java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2010 The Broad Institute
+ * Copyright (c) 2010.
  *
  * Permission is hereby granted, free of charge, to any person
  * obtaining a copy of this software and associated documentation
@@ -23,12 +23,11 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.gatk.walkers.sequenom;
+package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import org.broad.tribble.util.variantcontext.Allele;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broad.tribble.vcf.*;
-import org.broad.tribble.Feature;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
@@ -36,6 +35,8 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.QualityUtils;
+import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
@@ -46,8 +47,10 @@ import java.util.*;
  * Converts Sequenom files to a VCF annotated with QC metrics (HW-equilibrium, % failed probes)
  */
 @Reference(window=@Window(start=0,stop=40))
-@Requires(value={},referenceMetaData=@RMD(name="sequenom",type= Feature.class))
+@Requires(value={},referenceMetaData=@RMD(name=VariantValidationAssessor.INPUT_VARIANT_ROD_BINDING_NAME, type=VariantContext.class))
-public class SequenomValidationConverter extends RodWalker<Pair<VariantContext, Byte>,Integer> {
+public class VariantValidationAssessor extends RodWalker<Pair<VariantContext, Byte>,Integer> {
+
+    public static final String INPUT_VARIANT_ROD_BINDING_NAME = "variant";
 
     @Output(doc="File to which variants should be written",required=true)
     protected VCFWriter vcfwriter = null;
@@ -66,7 +69,7 @@ public class SequenomValidationConverter extends RodWalker<Pair<VariantContext,
     // sample names
     private TreeSet<String> sampleNames = null;
 
-    // vcf records
+    // variant context records
     private ArrayList<Pair<VariantContext, Byte>> records = new ArrayList<Pair<VariantContext, Byte>>();
 
     // statistics
@@ -85,28 +88,26 @@ public class SequenomValidationConverter extends RodWalker<Pair<VariantContext,
     }
 
     public Integer reduceInit() {
-        int numberOfVariantsProcessed = 0;
+        return 0;
-        return numberOfVariantsProcessed;
     }
 
     public Pair<VariantContext, Byte> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         if ( tracker == null )
             return null;
 
-        // get the sequenom rod at this locus if there is one
+        List<Object> rods = tracker.getReferenceMetaData(INPUT_VARIANT_ROD_BINDING_NAME);
-        List<Object> rods = tracker.getReferenceMetaData("sequenom");
         // ignore places where we don't have a variant
         if ( rods.size() == 0 )
             return null;
 
         Object rod = rods.get(0);
 
-        VariantContext vc = VariantContextAdaptors.toVariantContext("sequenom", rod, ref);
+        VariantContext vc = VariantContextAdaptors.toVariantContext(INPUT_VARIANT_ROD_BINDING_NAME, rod, ref);
 
         if ( sampleNames == null )
             sampleNames = new TreeSet<String>(vc.getSampleNames());        
 
-        return addVariantInformationToCall(ref, vc, rod);
+        return addVariantInformationToCall(ref, vc);
     }
 
     public Integer reduce(Pair<VariantContext, Byte> call, Integer numVariants) {
@@ -118,13 +119,14 @@ public class SequenomValidationConverter extends RodWalker<Pair<VariantContext,
     }
 
     public void onTraversalDone(Integer finalReduce) {
-        if ( sampleNames == null )
+        final ArrayList<String> inputNames = new ArrayList<String>();
-            sampleNames = new TreeSet<String>();
+        inputNames.add( INPUT_VARIANT_ROD_BINDING_NAME );
+
+        // setup the header fields
+        Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
+        hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames));
 
         // set up the info and filter headers
-        Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
-        hInfo.add(new VCFHeaderLine("source", "SequenomValidationConverter"));
-        hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
         hInfo.add(new VCFInfoHeaderLine("NoCallPct", 1, VCFHeaderLineType.Float, "Percent of no-calls"));
         hInfo.add(new VCFInfoHeaderLine("HomRefPct", 1, VCFHeaderLineType.Float, "Percent of homozygous reference genotypes"));
         hInfo.add(new VCFInfoHeaderLine("HetPct", 1, VCFHeaderLineType.Float, "Percent of heterozygous genotypes"));
@@ -157,15 +159,14 @@ public class SequenomValidationConverter extends RodWalker<Pair<VariantContext,
             }
         }
         
-        VCFHeader header = new VCFHeader(hInfo, sampleNames);
+        vcfwriter.writeHeader(new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames)));
-        vcfwriter.writeHeader(header);
 
         for ( Pair<VariantContext, Byte> record : records )
             vcfwriter.add(record.first, record.second);
     }
 
 
-    private Pair<VariantContext, Byte> addVariantInformationToCall(ReferenceContext ref, VariantContext vContext, Object rod) {
+    private Pair<VariantContext, Byte> addVariantInformationToCall(ReferenceContext ref, VariantContext vContext) {
 
         // check possible filters
         double hwPvalue = hardyWeinbergCalculation(vContext);

java/test/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverterIntegrationTest.java

@@ -1,32 +0,0 @@
-package org.broadinstitute.sting.gatk.walkers.sequenom;
-
-import org.broadinstitute.sting.WalkerTest;
-import org.junit.Test;
-
-import java.util.Arrays;
-
-public class SequenomValidationConverterIntegrationTest extends WalkerTest {
-
-    public void testEmpty() {
-        System.err.println("Reinstate these tests when plink is back in");
-    }
-
-    //@Test TODO: reinstate the test when the Plink rod is back
-    public void testSNPs() {
-        String testPedFile = validationDataLocation + "Sequenom_Test_File.txt";
-        String testArgs = "-R "+b36KGReference + " -T SequenomValidationConverter -B:sequenom,Plink "+testPedFile+" -o %s";
-        WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
-                Arrays.asList("2dab4630f40b76c0762de83fcbb60d09"));
-        executeTest("Test SNPs", spec);
-    }
-
-//    @Test
-    // TODO- need to be reenabled when PED reader tracks gets updated to read indels correctly
-    public void testIndels() {
-        String testPedFile = validationDataLocation + "pilot2_indel_validation.renamed.ped";
-        String testArgs = "-R "+b36KGReference + " -T SequenomValidationConverter -B:sequenom,Plink "+testPedFile+" -o %s";
-        WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
-                Arrays.asList("fad2dd71550dec064d458c4aa83e4de9"));
-        executeTest("Test Indels", spec);
-    }
-}

packages/GenomeAnalysisTK.xml

@@ -29,7 +29,6 @@
       <class name="org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker" />
       <class name="org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker" />
       <!-- Other misc walkers -->
-      <class name="org.broadinstitute.sting.gatk.walkers.sequenom.SequenomValidationConverter" />
       <class name="org.broadinstitute.sting.gatk.walkers.variantutils.CombineVariants" />
       <class name="org.broadinstitute.sting.gatk.walkers.VariantsToVCF" />
     </dependencies>