Package htsjdk.variant.vcf

Examples of htsjdk.variant.vcf.VCFHeader

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        verifySampleRenaming(outputVCF, "newSampleForNA12878");
    }

    private void verifySampleRenaming( final File outputVCF, final String newSampleName ) throws IOException {
        final Pair<VCFHeader, GATKVCFUtils.VCIterable<LineIterator>> headerAndVCIter = GATKVCFUtils.readAllVCs(outputVCF, new VCFCodec());
        final VCFHeader header = headerAndVCIter.getFirst();
        final GATKVCFUtils.VCIterable<LineIterator> iter = headerAndVCIter.getSecond();

        // Verify that sample renaming occurred at both the header and record levels (checking only the first 10 records):

        Assert.assertEquals(header.getGenotypeSamples().size(), 1, "Wrong number of samples in output vcf header");
        Assert.assertEquals(header.getGenotypeSamples().get(0), newSampleName, "Wrong sample name in output vcf header");

        int recordCount = 0;
        while ( iter.hasNext() && recordCount < 10 ) {
            final VariantContext vcfRecord = iter.next();
            Assert.assertEquals(vcfRecord.getSampleNames().size(), 1, "Wrong number of samples in output vcf record");
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    public static class VCFHeaderTest2Walker extends VCFHeaderTestWalker {}

    @Test
    public void testAddingVCFHeaderInfo() {
        final VCFHeader header = new VCFHeader();

        final Walker walker1 = new VCFHeaderTestWalker();
        final Walker walker2 = new VCFHeaderTest2Walker();

        final GenomeAnalysisEngine testEngine1 = new GenomeAnalysisEngine();
        testEngine1.setWalker(walker1);

        final GenomeAnalysisEngine testEngine2 = new GenomeAnalysisEngine();
        testEngine2.setWalker(walker2);

        final VCFHeaderLine line1 = GATKVCFUtils.getCommandLineArgumentHeaderLine(testEngine1, Collections.EMPTY_LIST);
        logger.warn(line1);
        Assert.assertNotNull(line1);
        Assert.assertEquals(line1.getKey(), GATKVCFUtils.GATK_COMMAND_LINE_KEY);
        for ( final String field : Arrays.asList("Version", "ID", "Date", "CommandLineOptions"))
            Assert.assertTrue(line1.toString().contains(field), "Couldn't find field " + field + " in " + line1.getValue());
        Assert.assertTrue(line1.toString().contains("ID=" + testEngine1.getWalkerName()));

        final VCFHeaderLine line2 = GATKVCFUtils.getCommandLineArgumentHeaderLine(testEngine2, Collections.EMPTY_LIST);
        logger.warn(line2);

        header.addMetaDataLine(line1);
        final Set<VCFHeaderLine> lines1 = header.getMetaDataInInputOrder();
        Assert.assertTrue(lines1.contains(line1));

        header.addMetaDataLine(line2);
        final Set<VCFHeaderLine> lines2 = header.getMetaDataInInputOrder();
        Assert.assertTrue(lines2.contains(line1));
        Assert.assertTrue(lines2.contains(line2));
    }
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            if(count%10 ==0)
                System.out.print(count);
            else
                System.out.print(".");
            if (firstFile){
                VCFHeader header = (VCFHeader)reader.getHeader();
                outputWriter.writeHeader(header);
                firstFile = false;
            }

            Iterator<VariantContext> it = reader.iterator();
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        if ( bootstrap < 0.0 | bootstrap > 1.0 )
            throw new UserException.BadArgumentValue("bootstrap", "Bootstrap value must be fraction between 0 and 1");

        if ( bootstrapVCFOutput != null ) {
            Set<VCFHeaderLine> hInfo = GATKVCFUtils.getHeaderFields(getToolkit());
            bootstrapVCFOutput.writeHeader(new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit())));
        }
    }
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        // setup the header fields
        Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
        hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), inputNames));
        hInfo.add(new VCFFilterHeaderLine("bootstrap","This site used for genotype bootstrapping with ProduceBeagleInputWalker"));

        bootstrapVCFOutput.writeHeader(new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames)));
    }
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        final Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName));

        final Map<String, VCFHeader> vcfHeaders = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));
        final Set<VCFHeaderLine> headerLines = vcfHeaders.get(trackName).getMetaDataInSortedOrder();

        baseWriter.writeHeader(new VCFHeader(headerLines, samples));

        vcfWriter = VariantContextWriterFactory.sortOnTheFly(baseWriter, 200);
    }
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        if(splitToMany){
            writers = new VariantContextWriter[numOfFiles];
            for(int i = 0; i<writers.length; i++){
                writers[i] = VariantContextWriterFactory.create(new File(baseFileName+".split."+i+".vcf"), getMasterSequenceDictionary());
                writers[i].writeHeader(new VCFHeader(hInfo,samples));
            }

        }
        else {
            vcfWriter1.writeHeader(new VCFHeader(hInfo, samples));
            vcfWriter2 = VariantContextWriterFactory.create(file2, getMasterSequenceDictionary());
            vcfWriter2.writeHeader(new VCFHeader(hInfo, samples));
        }
    }
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    public void initialize() {
        String trackName = variantCollection.variants.getName();
        Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName));
        Map<String, VCFHeader> vcfHeaders = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));

        final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey(trackName) ? vcfHeaders.get(trackName).getMetaDataInSortedOrder() : Collections.<VCFHeaderLine>emptySet(), samples);
        writer.writeHeader(vcfHeader);
    }
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        return VariantContextUtils.initializeMatchExps(dummyNames, genotypeFilterExpressions);
    }

    public ConcordanceMetrics reduceInit() {
        Map<String,VCFHeader> headerMap = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(evalBinding,compBinding));
        VCFHeader evalHeader = headerMap.get(evalBinding.getName());
        evalSamples = evalHeader.getGenotypeSamples();
        VCFHeader compHeader = headerMap.get(compBinding.getName());
        compSamples = compHeader.getGenotypeSamples();
        return new ConcordanceMetrics(evalHeader,compHeader, sitesFile);
    }
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        String trackName = variantCollection.variants.getName();
        Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName));
        Map<String, VCFHeader> vcfHeaders = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));

        Set<VCFHeaderLine> headerLines = vcfHeaders.get(trackName).getMetaDataInSortedOrder();
        baseWriter.writeHeader(new VCFHeader(headerLines, samples));

        writer = VariantContextWriterFactory.sortOnTheFly(baseWriter, 200);
    }
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Related Classes of htsjdk.variant.vcf.VCFHeader

  • bcbio.gatk.tools.walkers.LeftAlignVariants
  • org.broad.igv.track.TrackLoader
  • org.broad.igv.variant.vcf.VCFWriterTest
  • org.broadinstitute.gatk.engine.EngineFeaturesIntegrationTest
  • org.broadinstitute.gatk.tools.CatVariants
  • org.broadinstitute.gatk.tools.walkers.beagle.ProduceBeagleInput
  • org.broadinstitute.gatk.tools.walkers.beagle.VariantsToBeagleUnphased
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeResolver
  • org.broadinstitute.gatk.tools.walkers.phasing.MergeSegregatingAlternateAllelesVCFWriter
  • org.broadinstitute.gatk.tools.walkers.validation.validationsiteselector.ValidationSiteSelector
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