Examples with VCFIDHeaderLine htsjdk.variant.vcf.VCFIDHeaderLine used on opensource projects

Example 1 with VCFIDHeaderLine

use of htsjdk.variant.vcf.VCFIDHeaderLine in project gatk by broadinstitute.

the class GATKToolUnitTest method testGetDefaultToolVCFHeaderLines.

@Test
public void testGetDefaultToolVCFHeaderLines() throws IOException {
    final TestGATKToolWithFeatures tool = new TestGATKToolWithFeatures();
    final File vcfFile = new File(publicTestDir + "org/broadinstitute/hellbender/engine/feature_data_source_test_with_bigHeader.vcf");
    final String[] args = { "--mask", vcfFile.getCanonicalPath(), "--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "true" };
    tool.instanceMain(args);
    Set<VCFHeaderLine> stdHeaderLines = tool.getDefaultToolVCFHeaderLines();
    VCFHeader hdr = new VCFHeader(stdHeaderLines);
    VCFHeaderLine sourceLine = hdr.getOtherHeaderLine("source");
    Assert.assertEquals(sourceLine.getValue(), tool.getClass().getSimpleName());
    VCFIDHeaderLine commandLine = (VCFIDHeaderLine) hdr.getOtherHeaderLine("GATKCommandLine");
    Assert.assertEquals(commandLine.getID(), tool.getClass().getSimpleName());
    String commandLineString = commandLine.toString();
    assertContains(commandLineString, "CommandLine=");
    assertContains(commandLineString, "Version=");
    assertContains(commandLineString, "Date=");
}