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
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@ -1,7 +1,5 @@
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package org.broadinstitute.sting.gatk.refdata;
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import edu.mit.broad.picard.genotype.DiploidGenotype;
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import edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods;
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import org.broad.tribble.dbsnp.DbSNPFeature;
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import org.broad.tribble.gelitext.GeliTextFeature;
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import org.broad.tribble.hapmap.HapMapFeature;
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@ -114,15 +112,6 @@ public class VariantContextAdaptors {
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}
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}
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private static Allele deletionAllele(ReferenceContext ref, int start, int len) {
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byte[] deletion = new byte[len];
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System.arraycopy(ref.getBases(), start, deletion, 0, len);
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return Allele.create(deletion, true);
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}
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public static VCFHeader createVCFHeader(Set<VCFHeaderLine> hInfo, VariantContext vc) {
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HashSet<String> names = new LinkedHashSet<String>();
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for ( Genotype g : vc.getGenotypesSortedByName() ) {
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@ -28,7 +28,6 @@ package org.broadinstitute.sting.gatk.walkers.filters;
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import org.broad.tribble.util.variantcontext.Genotype;
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import org.broad.tribble.util.variantcontext.VariantContext;
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import org.broad.tribble.vcf.*;
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import org.broadinstitute.sting.commandline.Hidden;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
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@ -37,7 +36,6 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.commandline.CommandLineUtils;
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import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.vcf.VCFUtils;
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@ -1,5 +1,5 @@
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/*
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* Copyright (c) 2010 The Broad Institute
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* Copyright (c) 2010.
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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@ -23,12 +23,11 @@
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.walkers.sequenom;
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package org.broadinstitute.sting.gatk.walkers.variantutils;
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import org.broad.tribble.util.variantcontext.Allele;
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import org.broad.tribble.util.variantcontext.VariantContext;
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import org.broad.tribble.vcf.*;
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import org.broad.tribble.Feature;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
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@ -36,6 +35,8 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.utils.QualityUtils;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.vcf.VCFUtils;
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import org.broadinstitute.sting.utils.collections.Pair;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.commandline.Output;
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@ -46,8 +47,10 @@ import java.util.*;
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* Converts Sequenom files to a VCF annotated with QC metrics (HW-equilibrium, % failed probes)
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*/
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@Reference(window=@Window(start=0,stop=40))
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@Requires(value={},referenceMetaData=@RMD(name="sequenom",type= Feature.class))
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public class SequenomValidationConverter extends RodWalker<Pair<VariantContext, Byte>,Integer> {
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@Requires(value={},referenceMetaData=@RMD(name=VariantValidationAssessor.INPUT_VARIANT_ROD_BINDING_NAME, type=VariantContext.class))
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public class VariantValidationAssessor extends RodWalker<Pair<VariantContext, Byte>,Integer> {
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public static final String INPUT_VARIANT_ROD_BINDING_NAME = "variant";
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@Output(doc="File to which variants should be written",required=true)
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protected VCFWriter vcfwriter = null;
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@ -66,7 +69,7 @@ public class SequenomValidationConverter extends RodWalker<Pair<VariantContext,
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// sample names
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private TreeSet<String> sampleNames = null;
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// vcf records
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// variant context records
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private ArrayList<Pair<VariantContext, Byte>> records = new ArrayList<Pair<VariantContext, Byte>>();
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// statistics
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@ -85,28 +88,26 @@ public class SequenomValidationConverter extends RodWalker<Pair<VariantContext,
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}
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public Integer reduceInit() {
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int numberOfVariantsProcessed = 0;
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return numberOfVariantsProcessed;
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return 0;
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}
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public Pair<VariantContext, Byte> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( tracker == null )
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return null;
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// get the sequenom rod at this locus if there is one
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List<Object> rods = tracker.getReferenceMetaData("sequenom");
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List<Object> rods = tracker.getReferenceMetaData(INPUT_VARIANT_ROD_BINDING_NAME);
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// ignore places where we don't have a variant
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if ( rods.size() == 0 )
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return null;
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Object rod = rods.get(0);
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VariantContext vc = VariantContextAdaptors.toVariantContext("sequenom", rod, ref);
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VariantContext vc = VariantContextAdaptors.toVariantContext(INPUT_VARIANT_ROD_BINDING_NAME, rod, ref);
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if ( sampleNames == null )
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sampleNames = new TreeSet<String>(vc.getSampleNames());
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return addVariantInformationToCall(ref, vc, rod);
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return addVariantInformationToCall(ref, vc);
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}
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public Integer reduce(Pair<VariantContext, Byte> call, Integer numVariants) {
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@ -118,13 +119,14 @@ public class SequenomValidationConverter extends RodWalker<Pair<VariantContext,
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}
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public void onTraversalDone(Integer finalReduce) {
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if ( sampleNames == null )
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sampleNames = new TreeSet<String>();
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final ArrayList<String> inputNames = new ArrayList<String>();
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inputNames.add( INPUT_VARIANT_ROD_BINDING_NAME );
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// setup the header fields
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Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
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hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames));
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// set up the info and filter headers
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Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
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hInfo.add(new VCFHeaderLine("source", "SequenomValidationConverter"));
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hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
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hInfo.add(new VCFInfoHeaderLine("NoCallPct", 1, VCFHeaderLineType.Float, "Percent of no-calls"));
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hInfo.add(new VCFInfoHeaderLine("HomRefPct", 1, VCFHeaderLineType.Float, "Percent of homozygous reference genotypes"));
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hInfo.add(new VCFInfoHeaderLine("HetPct", 1, VCFHeaderLineType.Float, "Percent of heterozygous genotypes"));
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@ -157,15 +159,14 @@ public class SequenomValidationConverter extends RodWalker<Pair<VariantContext,
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}
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}
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VCFHeader header = new VCFHeader(hInfo, sampleNames);
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vcfwriter.writeHeader(header);
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vcfwriter.writeHeader(new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames)));
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for ( Pair<VariantContext, Byte> record : records )
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vcfwriter.add(record.first, record.second);
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}
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private Pair<VariantContext, Byte> addVariantInformationToCall(ReferenceContext ref, VariantContext vContext, Object rod) {
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private Pair<VariantContext, Byte> addVariantInformationToCall(ReferenceContext ref, VariantContext vContext) {
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// check possible filters
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double hwPvalue = hardyWeinbergCalculation(vContext);
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@ -1,32 +0,0 @@
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package org.broadinstitute.sting.gatk.walkers.sequenom;
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import org.broadinstitute.sting.WalkerTest;
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import org.junit.Test;
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import java.util.Arrays;
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public class SequenomValidationConverterIntegrationTest extends WalkerTest {
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public void testEmpty() {
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System.err.println("Reinstate these tests when plink is back in");
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}
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//@Test TODO: reinstate the test when the Plink rod is back
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public void testSNPs() {
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String testPedFile = validationDataLocation + "Sequenom_Test_File.txt";
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String testArgs = "-R "+b36KGReference + " -T SequenomValidationConverter -B:sequenom,Plink "+testPedFile+" -o %s";
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WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
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Arrays.asList("2dab4630f40b76c0762de83fcbb60d09"));
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executeTest("Test SNPs", spec);
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}
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// @Test
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// TODO- need to be reenabled when PED reader tracks gets updated to read indels correctly
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public void testIndels() {
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String testPedFile = validationDataLocation + "pilot2_indel_validation.renamed.ped";
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String testArgs = "-R "+b36KGReference + " -T SequenomValidationConverter -B:sequenom,Plink "+testPedFile+" -o %s";
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WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
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Arrays.asList("fad2dd71550dec064d458c4aa83e4de9"));
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executeTest("Test Indels", spec);
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}
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}
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@ -29,7 +29,6 @@
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<class name="org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker" />
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<class name="org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker" />
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<!-- Other misc walkers -->
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<class name="org.broadinstitute.sting.gatk.walkers.sequenom.SequenomValidationConverter" />
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<class name="org.broadinstitute.sting.gatk.walkers.variantutils.CombineVariants" />
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<class name="org.broadinstitute.sting.gatk.walkers.VariantsToVCF" />
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</dependencies>
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