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

Example 6 with GenomeLocParser

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

the class AssemblyResultSetUnitTest method init.

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

Example 7 with GenomeLocParser

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

the class BaseTest method initGenomeLocParser.

@BeforeClass
public void initGenomeLocParser() throws FileNotFoundException {
    hg19ReferenceReader = new CachingIndexedFastaSequenceFile(new File(hg19MiniReference));
    hg19Header = new SAMFileHeader();
    hg19Header.setSequenceDictionary(hg19ReferenceReader.getSequenceDictionary());
    hg19GenomeLocParser = new GenomeLocParser(hg19ReferenceReader);
}

Example 8 with GenomeLocParser

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

the class LocusIteratorByStateBaseTest method beforeClass.

@BeforeClass
public void beforeClass() {
    header = ArtificialReadUtils.createArtificialSamHeader(1, 1, 1000);
    genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
}