Examples with CachingIndexedFastaSequenceFile org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile used on opensource projects

Example 6 with CachingIndexedFastaSequenceFile

use of org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile in project gatk by broadinstitute.

the class ReadUtilsUnitTest method testReadWithNsRefIndexInDeletion.

@Test
public void testReadWithNsRefIndexInDeletion() throws FileNotFoundException {
    final IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(exampleReference));
    final SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeader(seq.getSequenceDictionary());
    final int readLength = 76;
    final GATKRead read = ArtificialReadUtils.createArtificialRead(header, "myRead", 0, 8975, readLength);
    read.setBases(Utils.dupBytes((byte) 'A', readLength));
    read.setBaseQualities(Utils.dupBytes((byte) 30, readLength));
    read.setCigar("3M414N1D73M");
    final int result = ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(read, 9392, ReadUtils.ClippingTail.LEFT_TAIL);
    Assert.assertEquals(result, 2);
}

Example 7 with CachingIndexedFastaSequenceFile

use of org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile in project gatk by broadinstitute.

the class ReadUtilsUnitTest method testReadWithNsRefAfterDeletion.

@Test
public void testReadWithNsRefAfterDeletion() throws FileNotFoundException {
    final IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(exampleReference));
    final SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeader(seq.getSequenceDictionary());
    final int readLength = 76;
    final GATKRead read = ArtificialReadUtils.createArtificialRead(header, "myRead", 0, 8975, readLength);
    read.setBases(Utils.dupBytes((byte) 'A', readLength));
    read.setBaseQualities(Utils.dupBytes((byte) 30, readLength));
    read.setCigar("3M414N1D73M");
    final int result = ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(read, 9393, ReadUtils.ClippingTail.LEFT_TAIL);
    Assert.assertEquals(result, 3);
}

Example 8 with CachingIndexedFastaSequenceFile

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

the class HaplotypeCaller method getReferenceReader.

private static CachingIndexedFastaSequenceFile getReferenceReader(ReferenceInputArgumentCollection referenceArguments) {
    final CachingIndexedFastaSequenceFile referenceReader;
    final File reference = new File(referenceArguments.getReferenceFileName());
    try {
        referenceReader = new CachingIndexedFastaSequenceFile(reference);
    } catch (FileNotFoundException e) {
        throw new UserException.CouldNotReadInputFile(reference, e);
    }
    return referenceReader;
}

Example 9 with CachingIndexedFastaSequenceFile

use of org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile 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 10 with CachingIndexedFastaSequenceFile

use of org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile 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));
}