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Example 46 with CommandLineArgumentParser

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

the class ReferenceInputArgumentCollectionTest method testRequiredIsRequired.

@Test(expectedExceptions = CommandLineException.class)
public void testRequiredIsRequired() {
    String[] args = {};
    WithRequiredReferenceCollection required = new WithRequiredReferenceCollection();
    CommandLineParser clp = new CommandLineArgumentParser(required);
    clp.parseArguments(System.out, args);
}
Also used : CommandLineArgumentParser(org.broadinstitute.barclay.argparser.CommandLineArgumentParser) CommandLineParser(org.broadinstitute.barclay.argparser.CommandLineParser) Test(org.testng.annotations.Test)

Example 47 with CommandLineArgumentParser

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

the class IntervalArgumentCollectionTest method testRequiredIsRequired.

@Test(expectedExceptions = CommandLineException.class)
public void testRequiredIsRequired() {
    WithRequiredIntervals opt = new WithRequiredIntervals();
    CommandLineParser clp = new CommandLineArgumentParser(opt);
    String[] args = {};
    clp.parseArguments(System.out, args);
}
Also used : CommandLineArgumentParser(org.broadinstitute.barclay.argparser.CommandLineArgumentParser) CommandLineParser(org.broadinstitute.barclay.argparser.CommandLineParser) BaseTest(org.broadinstitute.hellbender.utils.test.BaseTest) Test(org.testng.annotations.Test)

Aggregations

CommandLineArgumentParser (org.broadinstitute.barclay.argparser.CommandLineArgumentParser)47 CommandLineParser (org.broadinstitute.barclay.argparser.CommandLineParser)47 Test (org.testng.annotations.Test)44 GATKReadFilterPluginDescriptor (org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterPluginDescriptor)25 BaseTest (org.broadinstitute.hellbender.utils.test.BaseTest)13 File (java.io.File)11 IndexedFastaSequenceFile (htsjdk.samtools.reference.IndexedFastaSequenceFile)9 GATKRead (org.broadinstitute.hellbender.utils.read.GATKRead)7 SAMFileHeader (htsjdk.samtools.SAMFileHeader)6 SAMSequenceDictionary (htsjdk.samtools.SAMSequenceDictionary)6 ArrayList (java.util.ArrayList)6 List (java.util.List)3 ArgumentsBuilder (org.broadinstitute.hellbender.utils.test.ArgumentsBuilder)3 Assert (org.testng.Assert)3 SamReader (htsjdk.samtools.SamReader)2 VariantContext (htsjdk.variant.variantcontext.VariantContext)2 VCFFileReader (htsjdk.variant.vcf.VCFFileReader)2 Iterator (java.util.Iterator)2 Argument (org.broadinstitute.barclay.argparser.Argument)2 CommandLineProgramProperties (org.broadinstitute.barclay.argparser.CommandLineProgramProperties)2