Examples with ReferenceSequenceFile htsjdk.samtools.reference.ReferenceSequenceFile used on opensource projects

Example 11 with ReferenceSequenceFile

use of htsjdk.samtools.reference.ReferenceSequenceFile in project gatk by broadinstitute.

the class ActivityProfileUnitTest method init.

@BeforeClass
public void init() throws FileNotFoundException {
    // sequence
    ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37_reference_20_21));
    genomeLocParser = new GenomeLocParser(seq);
    startLoc = genomeLocParser.createGenomeLoc("20", 0, 1, 100);
    header = new SAMFileHeader();
    seq.getSequenceDictionary().getSequences().forEach(sequence -> header.addSequence(sequence));
}

Example 12 with ReferenceSequenceFile

use of htsjdk.samtools.reference.ReferenceSequenceFile in project gatk by broadinstitute.

the class BandPassActivityProfileUnitTest method init.

@BeforeClass
public void init() throws FileNotFoundException {
    // sequence
    ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37_reference_20_21));
    genomeLocParser = new GenomeLocParser(seq);
    header = new SAMFileHeader();
    seq.getSequenceDictionary().getSequences().forEach(sequence -> header.addSequence(sequence));
}

Example 13 with ReferenceSequenceFile

use of htsjdk.samtools.reference.ReferenceSequenceFile in project gatk-protected by broadinstitute.

the class HaplotypeCaller method onTraversalStart.

@Override
public void onTraversalStart() {
    final ReferenceSequenceFile referenceReader = getReferenceReader(referenceArguments);
    hcEngine = new HaplotypeCallerEngine(hcArgs, getHeaderForReads(), referenceReader);
    // The HC engine will make the right kind (VCF or GVCF) of writer for us
    final SAMSequenceDictionary sequenceDictionary = getHeaderForReads().getSequenceDictionary();
    vcfWriter = hcEngine.makeVCFWriter(outputVCF, sequenceDictionary);
    hcEngine.writeHeader(vcfWriter, sequenceDictionary, getDefaultToolVCFHeaderLines());
}

Example 14 with ReferenceSequenceFile

use of htsjdk.samtools.reference.ReferenceSequenceFile in project gatk by broadinstitute.

the class AssemblyBasedCallerUtils method assembleReads.

/**
     * High-level function that runs the assembler on the given region's reads,
     * returning a data structure with the resulting information needed
     * for further HC steps
     */
public static AssemblyResultSet assembleReads(final AssemblyRegion region, final List<VariantContext> givenAlleles, final AssemblyBasedCallerArgumentCollection argumentCollection, final SAMFileHeader header, final SampleList sampleList, final Logger logger, final ReferenceSequenceFile referenceReader, final ReadThreadingAssembler assemblyEngine) {
    finalizeRegion(region, argumentCollection.errorCorrectReads, argumentCollection.dontUseSoftClippedBases, (byte) (argumentCollection.minBaseQualityScore - 1), header, sampleList);
    if (argumentCollection.debug) {
        logger.info("Assembling " + region.getSpan() + " with " + region.size() + " reads:    (with overlap region = " + region.getExtendedSpan() + ")");
    }
    final byte[] fullReferenceWithPadding = region.getAssemblyRegionReference(referenceReader, REFERENCE_PADDING_FOR_ASSEMBLY);
    final SimpleInterval paddedReferenceLoc = getPaddedReferenceLoc(region, REFERENCE_PADDING_FOR_ASSEMBLY, referenceReader);
    final Haplotype referenceHaplotype = createReferenceHaplotype(region, paddedReferenceLoc, referenceReader);
    final ReadErrorCorrector readErrorCorrector = argumentCollection.errorCorrectReads ? new ReadErrorCorrector(argumentCollection.assemblerArgs.kmerLengthForReadErrorCorrection, HaplotypeCallerEngine.MIN_TAIL_QUALITY_WITH_ERROR_CORRECTION, argumentCollection.assemblerArgs.minObservationsForKmerToBeSolid, argumentCollection.debug, fullReferenceWithPadding) : null;
    try {
        final AssemblyResultSet assemblyResultSet = assemblyEngine.runLocalAssembly(region, referenceHaplotype, fullReferenceWithPadding, paddedReferenceLoc, givenAlleles, readErrorCorrector, header);
        assemblyResultSet.debugDump(logger);
        return assemblyResultSet;
    } catch (final Exception e) {
        // Capture any exception that might be thrown, and write out the assembly failure BAM if requested
        if (argumentCollection.captureAssemblyFailureBAM) {
            try (final SAMFileWriter writer = ReadUtils.createCommonSAMWriter(new File("assemblyFailure.bam"), null, header, false, false, false)) {
                for (final GATKRead read : region.getReads()) {
                    writer.addAlignment(read.convertToSAMRecord(header));
                }
            }
        }
        throw e;
    }
}

Example 15 with ReferenceSequenceFile

use of htsjdk.samtools.reference.ReferenceSequenceFile in project gatk by broadinstitute.

the class HaplotypeCaller method onTraversalStart.

@Override
public void onTraversalStart() {
    final ReferenceSequenceFile referenceReader = getReferenceReader(referenceArguments);
    hcEngine = new HaplotypeCallerEngine(hcArgs, getHeaderForReads(), referenceReader);
    // The HC engine will make the right kind (VCF or GVCF) of writer for us
    final SAMSequenceDictionary sequenceDictionary = getHeaderForReads().getSequenceDictionary();
    vcfWriter = hcEngine.makeVCFWriter(outputVCF, sequenceDictionary);
    hcEngine.writeHeader(vcfWriter, sequenceDictionary, getDefaultToolVCFHeaderLines());
}