Examples with CommandLineParser org.broadinstitute.barclay.argparser.CommandLineParser used on opensource projects

Example 26 with CommandLineParser

use of org.broadinstitute.barclay.argparser.CommandLineParser in project gatk by broadinstitute.

the class GATKToolUnitTest method testReadsHeader.

@Test
public void testReadsHeader() throws Exception {
    final GATKTool tool = new TestGATKToolWithReads();
    final CommandLineParser clp = new CommandLineArgumentParser(tool);
    final File bamFile = new File(publicTestDir + "org/broadinstitute/hellbender/engine/reads_data_source_test1.bam");
    final String[] args = { "-I", bamFile.getCanonicalPath() };
    clp.parseArguments(System.out, args);
    tool.onStartup();
    final SAMFileHeader headerForReads = tool.getHeaderForReads();
    final SamReaderFactory factory = //read the file directly and compare headers
    SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
    try (SamReader samReader = factory.open(bamFile)) {
        final SAMFileHeader samFileHeader = samReader.getFileHeader();
        Assert.assertEquals(headerForReads, samFileHeader);
    }
    tool.doWork();
    tool.onShutdown();
}

Example 27 with CommandLineParser

use of org.broadinstitute.barclay.argparser.CommandLineParser in project gatk by broadinstitute.

the class GATKToolUnitTest method testAllowLexicographicallySortedVariantHeader.

@Test
public void testAllowLexicographicallySortedVariantHeader() throws Exception {
    final GATKTool tool = new TestGATKToolWithFeatures();
    final CommandLineParser clp = new CommandLineArgumentParser(tool);
    final File vcfFile = new File(publicTestDir + "org/broadinstitute/hellbender/engine/lexicographically_sorted_dict.vcf");
    final String[] args = { "--mask", vcfFile.getCanonicalPath() };
    clp.parseArguments(System.out, args);
    // This method would throw if sequence dictionary validation failed. Here we are testing
    // that it does not throw despite the lexicographically-sorted sequence dictionary in the vcf.
    tool.onStartup();
}

Example 28 with CommandLineParser

use of org.broadinstitute.barclay.argparser.CommandLineParser in project gatk by broadinstitute.

the class GATKToolUnitTest method testNonExistentReferenceFile.

@Test(expectedExceptions = UserException.MissingReference.class)
public void testNonExistentReferenceFile() throws Exception {
    final TestGATKToolWithFeatures tool = new TestGATKToolWithFeatures();
    final CommandLineParser clp = new CommandLineArgumentParser(tool);
    final String[] args = { "--reference", BaseTest.getSafeNonExistentFile("NonExistentReferenceFile.fasta").getAbsolutePath() };
    clp.parseArguments(System.out, args);
    tool.onStartup();
}

Example 29 with CommandLineParser

use of org.broadinstitute.barclay.argparser.CommandLineParser in project gatk by broadinstitute.

the class GATKToolUnitTest method testBestSequenceDictionary_fromReadsAndReference.

@Test
public void testBestSequenceDictionary_fromReadsAndReference() throws Exception {
    final GATKTool tool = new TestGATKToolWithReads();
    final CommandLineParser clp = new CommandLineArgumentParser(tool);
    final File bamFile = new File(publicTestDir + "org/broadinstitute/hellbender/engine/reads_data_source_test1.bam");
    final String fastaFile = hg19MiniReference;
    final String[] args = { "-I", bamFile.getCanonicalPath(), "-R", fastaFile };
    clp.parseArguments(System.out, args);
    tool.onStartup();
    //read the dict back in and compare to reference dict
    final SAMSequenceDictionary toolDict = tool.getBestAvailableSequenceDictionary();
    final SAMSequenceDictionary fastaDict = new IndexedFastaSequenceFile(new File(fastaFile)).getSequenceDictionary();
    toolDict.assertSameDictionary(fastaDict);
    fastaDict.assertSameDictionary(toolDict);
    Assert.assertEquals(toolDict, fastaDict);
}

Example 30 with CommandLineParser

use of org.broadinstitute.barclay.argparser.CommandLineParser in project gatk by broadinstitute.

the class ReadInputArgumentCollectionTest method testRequiredIsRequired.

@Test(expectedExceptions = CommandLineException.class)
public void testRequiredIsRequired() {
    Object req = new Object() {

        @ArgumentCollection
        private ReadInputArgumentCollection ric = new RequiredReadInputArgumentCollection();
    };
    CommandLineParser clp = new CommandLineArgumentParser(req);
    String[] args = {};
    clp.parseArguments(System.out, args);
}