Examples with GenomeLocParser org.broadinstitute.hellbender.utils.GenomeLocParser used on opensource projects

Example 1 with GenomeLocParser

use of org.broadinstitute.hellbender.utils.GenomeLocParser in project gatk by broadinstitute.

the class ReferenceConfidenceModelUnitTest method setUp.

@BeforeClass
public void setUp() {
    header = ArtificialReadUtils.createArtificialSamHeader(1, 1, 1000);
    rg = new SAMReadGroupRecord(RGID);
    rg.setSample(sample);
    header.addReadGroup(rg);
    parser = new GenomeLocParser(header.getSequenceDictionary());
}

Example 2 with GenomeLocParser

use of org.broadinstitute.hellbender.utils.GenomeLocParser in project gatk by broadinstitute.

the class AssemblyResultSetUnitTest method init.

@BeforeClass
public void init() {
    header = ArtificialReadUtils.createArtificialSamHeader(1, 1, 1000000);
    genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
}

Example 3 with GenomeLocParser

use of org.broadinstitute.hellbender.utils.GenomeLocParser in project gatk by broadinstitute.

the class SplitNCigarReads method onTraversalStart.

@Override
public void onTraversalStart() {
    header = getHeaderForSAMWriter();
    rnaReadTransform = REFACTOR_NDN_CIGAR_READS ? new NDNCigarReadTransformer() : ReadTransformer.identity();
    try {
        referenceReader = new CachingIndexedFastaSequenceFile(referenceArguments.getReferenceFile());
        GenomeLocParser genomeLocParser = new GenomeLocParser(getBestAvailableSequenceDictionary());
        outputWriter = createSAMWriter(OUTPUT, false);
        overhangManager = new OverhangFixingManager(header, outputWriter, genomeLocParser, referenceReader, MAX_RECORDS_IN_MEMORY, MAX_MISMATCHES_IN_OVERHANG, MAX_BASES_TO_CLIP, doNotFixOverhangs, processSecondaryAlignments);
    } catch (FileNotFoundException ex) {
        throw new UserException.CouldNotReadInputFile(referenceArguments.getReferenceFile(), ex);
    }
}

Example 4 with GenomeLocParser

use of org.broadinstitute.hellbender.utils.GenomeLocParser in project gatk-protected by broadinstitute.

the class ReferenceConfidenceModelUnitTest method setUp.

@BeforeClass
public void setUp() {
    header = ArtificialReadUtils.createArtificialSamHeader(1, 1, 1000);
    rg = new SAMReadGroupRecord(RGID);
    rg.setSample(sample);
    header.addReadGroup(rg);
    parser = new GenomeLocParser(header.getSequenceDictionary());
}

Example 5 with GenomeLocParser

use of org.broadinstitute.hellbender.utils.GenomeLocParser 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));
}