Package org.broadinstitute.gatk.utils

Examples of org.broadinstitute.gatk.utils.GenomeLocParser

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    private GenomeLocParser createGenomeLocParser() {
        SAMSequenceDictionary dict = new SAMSequenceDictionary();
        for (Chromosome chr : GenomeManager.getInstance().getCurrentGenome().getChromosomes()) {
            dict.addSequence(new SAMSequenceRecord(chromoNameToStandard(chr.getName()), chr.getLength()));
        }
        return new GenomeLocParser(dict);
    }
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            SCAC.setSampleContamination(AlleleBiasedDownsamplingUtils.loadContaminationFile(SCAC.CONTAMINATION_FRACTION_FILE, SCAC.CONTAMINATION_FRACTION, sampleSet, logger));

        if( SCAC.genotypingOutputMode == GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES && consensusMode )
            throw new UserException("HaplotypeCaller cannot be run in both GENOTYPE_GIVEN_ALLELES mode and in consensus mode at the same time. Please choose one or the other.");

        final GenomeLocParser genomeLocParser = toolkit.getGenomeLocParser();

        genotypingEngine = new HaplotypeCallerGenotypingEngine( SCAC, samplesList, genomeLocParser, FixedAFCalculatorProvider.createThreadSafeProvider(getToolkit(),SCAC,logger), !doNotRunPhysicalPhasing);
        // initialize the output VCF header
        final VariantAnnotatorEngine annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit());
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        for ( int i = 3; i < args.length; i++ )
            startsToUse.add(Integer.valueOf(args[i]));

        final CachingIndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(ref);
        final GenomeLocParser parser = new GenomeLocParser(seq);
        final BufferedReader reader = new BufferedReader(new FileReader(exactLogFile));
        final List<ExactCallLogger.ExactCall> loggedCalls = ExactCallLogger.readExactLog(reader, startsToUse, parser);

        for ( final ExactCallLogger.ExactCall call : loggedCalls ) {
            final AFCalculatorTestBuilder testBuilder = new AFCalculatorTestBuilder(call.vc.getNSamples(), 1,
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    @BeforeClass
    public void setup() throws FileNotFoundException {
        // sequence
        seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        genomeLocParser = new GenomeLocParser(seq);
    }
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    private GenomeLocParser genomeLocParser;

    @BeforeClass
    public void setup() throws FileNotFoundException {
        referenceReader = new CachingIndexedFastaSequenceFile(new File(hg18Reference));
        genomeLocParser = new GenomeLocParser(referenceReader.getSequenceDictionary());
    }
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    private GenomeLocParser genomeLocParser;

    @BeforeClass
    public void setup() throws FileNotFoundException {
        referenceReader = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        genomeLocParser = new GenomeLocParser(referenceReader.getSequenceDictionary());
    }
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        // if cds file is not provided, just use the targets file (no harm done)
        if (baitsFile == null)
            baitsFile = targetsFile;

        simpleReport = GATKReport.newSimpleReport("QualifyMissingIntervals", "INTERVAL", "GC", "BQ", "MQ", "DP", "POS_IN_TARGET", "TARGET_SIZE", "BAITED", "MISSING_SIZE", "INTERPRETATION");
        final GenomeLocParser parser = getToolkit().getGenomeLocParser();
        targets = new GenomeLocSortedSet(parser, IntervalUtils.intervalFileToList(parser, targetsFile));
        baits = new GenomeLocSortedSet(parser, IntervalUtils.intervalFileToList(parser, baitsFile));
    }
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    }

    private void HCTestNearbySmallIntervals(String bam, String args, String md5) {
        try {
            final IndexedFastaSequenceFile fasta = new IndexedFastaSequenceFile(new File(b37KGReference));
            final GenomeLocParser parser = new GenomeLocParser(fasta.getSequenceDictionary());

            final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R %s -I %s", REF, bam) + " -L 20:10,001,603-10,001,642 -L 20:10,001,653-10,001,742 --no_cmdline_in_header -o %s";
            final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
            for( final File vcf : executeTest("testHaplotypeCallerNearbySmallIntervals: args=" + args, spec).getFirst() ) {
                if( containsDuplicateRecord(vcf, parser) ) {
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    @BeforeClass
    public void setup() throws FileNotFoundException {
        // sequence
        seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        genomeLocParser = new GenomeLocParser(seq);
    }
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    private SAMFileHeader header;

    @BeforeClass
    public void init() {
        header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000000);
        genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
    }
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Related Classes of org.broadinstitute.gatk.utils.GenomeLocParser

  • htsjdk.samtools.SAMSequenceRecord
  • org.broad.igv.plugin.mongovariant.VariantReviewSource
  • org.broadinstitute.gatk.engine.datasources.providers.IntervalReferenceOrderedViewUnitTest
  • org.broadinstitute.gatk.engine.datasources.providers.LocusViewTemplate
  • org.broadinstitute.gatk.engine.datasources.providers.ReferenceOrderedViewUnitTest
  • org.broadinstitute.gatk.engine.datasources.providers.ReferenceViewTemplate
  • org.broadinstitute.gatk.engine.datasources.reads.ActiveRegionShardBalancerUnitTest
  • org.broadinstitute.gatk.engine.datasources.reads.FilePointerUnitTest
  • org.broadinstitute.gatk.engine.datasources.reads.IntervalOverlapFilteringIteratorUnitTest
  • org.broadinstitute.gatk.engine.datasources.reads.ReadShardBalancerUnitTest$ReadShardBalancerTest
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