Examples with SAMFileHeader htsjdk.samtools.SAMFileHeader used on opensource projects

Example 96 with SAMFileHeader

use of htsjdk.samtools.SAMFileHeader in project gatk by broadinstitute.

the class SATagBuilderUnitTests method testEmptyNMTagSupport.

@Test
public void testEmptyNMTagSupport() {
    SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeader();
    GATKRead read = ArtificialReadUtils.createArtificialRead(header, "name", "2", 1, "AAAAAAAAAA".getBytes(), "##########".getBytes());
    read.setAttribute("SA", "1,191,-,8M2S,60,*;");
    List<GATKRead> reads = (new SATagBuilder(read)).getArtificialReadsBasedOnSATag(header);
    Assert.assertFalse(reads.get(0).hasAttribute("NM"));
}

Example 97 with SAMFileHeader

use of htsjdk.samtools.SAMFileHeader 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 98 with SAMFileHeader

use of htsjdk.samtools.SAMFileHeader 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 99 with SAMFileHeader

use of htsjdk.samtools.SAMFileHeader in project gatk by broadinstitute.

the class ReadClipperUnitTest method testSoftClippingOpEdgeCase.

// This test depends on issue #2022 as it tests the current behavior of the clipping operation
@Test
public void testSoftClippingOpEdgeCase() {
    final SAMFileHeader header = new SAMFileHeader();
    header.setSequenceDictionary(hg19GenomeLocParser.getSequenceDictionary());
    GATKRead read = ReadClipperTestUtils.makeReadFromCigar("8M");
    ReadClipper clipper = new ReadClipper(read);
    ClippingOp op = new ClippingOp(0, 7);
    clipper.addOp(op);
    GATKRead softResult = clipper.clipRead(ClippingRepresentation.SOFTCLIP_BASES);
    Assert.assertEquals(softResult.getCigar().toString(), "7S1M");
}

Example 100 with SAMFileHeader

use of htsjdk.samtools.SAMFileHeader in project gatk by broadinstitute.

the class ActivityProfileStateUnitTest method init.

@BeforeClass
public void init() {
    // sequence
    final SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeader(1, 1, 100);
    sequenceDictionary = header.getSequenceDictionary();
}