Moved (poorly named) MergeAndMatchHaplotypes to public. Added integration test
This commit is contained in:
Kiran V Garimella
parent
afb506e128
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8167aba601
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package org.broadinstitute.sting.gatk.walkers.phasing;
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import org.broadinstitute.sting.commandline.Output;
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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.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
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import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
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import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
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import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
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import org.broadinstitute.sting.utils.variantcontext.Allele;
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import org.broadinstitute.sting.utils.variantcontext.Genotype;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
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import java.util.*;
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public class MergeAndMatchHaplotypes extends RodWalker<Integer, Integer> {
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@Output
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protected VCFWriter vcfWriter = null;
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private Map<String, Genotype> pbtCache = new HashMap<String, Genotype>();
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private Map<String, Genotype> rbpCache = new HashMap<String, Genotype>();
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private final String SOURCE_NAME = "MergeReadBackedAndTransmissionPhasedVariants";
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public void initialize() {
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ArrayList<String> rodNames = new ArrayList<String>();
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rodNames.add("pbt");
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Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames);
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Set<String> vcfSamples = SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
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Set<VCFHeaderLine> headerLines = new HashSet<VCFHeaderLine>();
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headerLines.addAll(VCFUtils.getHeaderFields(this.getToolkit()));
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vcfWriter.writeHeader(new VCFHeader(headerLines, vcfSamples));
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}
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@Override
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if (tracker != null) {
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Collection<VariantContext> pbts = tracker.getVariantContexts(ref, "pbt", null, ref.getLocus(), true, true);
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Collection<VariantContext> rbps = tracker.getVariantContexts(ref, "rbp", null, ref.getLocus(), true, true);
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VariantContext pbt = pbts.iterator().hasNext() ? pbts.iterator().next() : null;
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VariantContext rbp = rbps.iterator().hasNext() ? rbps.iterator().next() : null;
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if (pbt != null && rbp != null) {
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Map<String, Genotype> genotypes = pbt.getGenotypes();
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if (!rbp.isFiltered()) {
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for (String sample : rbp.getSampleNames()) {
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Genotype rbpg = rbp.getGenotype(sample);
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Genotype pbtg = pbt.getGenotype(sample);
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// Propagate read-backed phasing information to genotypes unphased by transmission
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//if (!pbtg.isPhased() && rbpCache.containsKey(sample)) {
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if (!pbtg.isPhased() && rbpg.isPhased() && rbpCache.containsKey(sample)) {
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boolean orientationMatches = rbpCache.get(sample).sameGenotype(pbtCache.get(sample), false);
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if (orientationMatches) {
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pbtg = rbpg;
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} else {
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List<Allele> fwdAlleles = rbpg.getAlleles();
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List<Allele> revAlleles = new ArrayList<Allele>();
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for (int i = fwdAlleles.size() - 1; i >= 0; i--) {
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revAlleles.add(fwdAlleles.get(i));
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}
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pbtg = new Genotype(sample, revAlleles, rbpg.getNegLog10PError(), rbpg.getFilters(), rbpg.getAttributes(), rbpg.isPhased());
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}
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}
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genotypes.put(sample, pbtg);
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// Update the cache
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if (/*rbpg.isPhased() &&*/ rbpg.isHet()) {
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rbpCache.put(sample, rbpg);
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pbtCache.put(sample, pbtg);
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} else if (!rbpg.isPhased()) {
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rbpCache.remove(sample);
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pbtCache.remove(sample);
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}
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}
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}
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VariantContext newvc = new VariantContext(SOURCE_NAME, pbt.getChr(), pbt.getStart(), pbt.getStart(), pbt.getAlleles(), genotypes, pbt.getNegLog10PError(), pbt.getFilters(), pbt.getAttributes());
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vcfWriter.add(newvc, ref.getBase());
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}
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}
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return null;
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}
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@Override
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public Integer reduceInit() {
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return null;
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}
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@Override
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public Integer reduce(Integer value, Integer sum) {
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return null;
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}
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}
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@ -0,0 +1,28 @@
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package org.broadinstitute.sting.gatk.walkers.phasing;
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import org.broadinstitute.sting.WalkerTest;
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import org.testng.annotations.Test;
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import java.util.Arrays;
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public class MergeAndMatchHaplotypesIntegrationTest extends WalkerTest {
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private static String mergeAndMatchHaplotypesTestDataRoot = validationDataLocation + "/MergeByHaplotypes";
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private static String fundamentalTestPBTVCF = mergeAndMatchHaplotypesTestDataRoot + "/" + "FundamentalsTest.pbt.vcf";
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private static String fundamentalTestRBPVCF = mergeAndMatchHaplotypesTestDataRoot + "/" + "FundamentalsTest.pbt.rbp.vcf";
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@Test
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public void testBasicFunctionality() {
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WalkerTestSpec spec = new WalkerTestSpec(
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buildCommandLine(
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"-T MergeAndMatchHaplotypes",
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"-R " + b37KGReference,
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"-B:pbt,VCF " + fundamentalTestPBTVCF,
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"-B:rbp,VCF " + fundamentalTestRBPVCF,
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"-o %s"
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),
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1,
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Arrays.asList("")
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);
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executeTest("testBasicMergeAndMatchHaplotypesFunctionality", spec);
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}
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}
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