Examples with BuildBamIndex picard.sam.BuildBamIndex used on opensource projects

Example 1 with BuildBamIndex

use of picard.sam.BuildBamIndex in project gridss by PapenfussLab.

the class StaticDeBruijnPathGraphGexfExporterTest method positional_should_export_dot.

@Test
@Category(Hg19Tests.class)
public void positional_should_export_dot() throws IOException {
    File output = new File(super.testFolder.getRoot(), "chr12-244000.vcf");
    setReference(Hg19Tests.findHg19Reference("chr12.fa"));
    createInput(new File("src/test/resources/chr12-244000.tagged.bam"));
    BuildBamIndex bbi = new BuildBamIndex();
    bbi.instanceMain(new String[] { "I=" + input.getAbsolutePath() });
    ProcessingContext pc = getCommandlineContext();
    SAMEvidenceSource ses = new SAMEvidenceSource(pc, input, null, 0);
    AssemblyEvidenceSource aes = new AssemblyEvidenceSource(pc, ImmutableList.of(ses), output);
    aes.assembleBreakends(null);
    File dir = new File(super.testFolder.getRoot(), "visualisation");
    File[] export = dir.listFiles((FileFilter) new WildcardFileFilter("*.dot"));
    // TODO: change graph write timing
    assertTrue(export != null && export.length > 0);
}