Examples of org.broadinstitute.gatk.engine.CommandLineGATK

org.broadinstitute.gatk.engine.CommandLineGATK
All command line parameters accepted by all tools in the GATK.
Info for general users

This is a list of options and parameters that are generally available to all tools in the GATK.

There may be a few restrictions, which are indicated in individual argument descriptions. For example the -BQSR argument is only meant to be used with a subset of tools, and the -pedigree argument will only be effectively used by a subset of tools as well. Some arguments conflict with others, and some conversely are dependent on others. This is all indicated in the detailed argument descriptions, so be sure to read those in their entirety rather than just skimming the one-line summaey in the table.

Info for developers

This class is the GATK engine itself, which manages map/reduce data access and runs walkers.

We run command line GATK programs using this class. It gets the command line args, parses them, and hands the gatk all the parsed out information. Pretty much anything dealing with the underlying system should go here; the GATK engine should deal with any data related information.

     * @param testClassName the name of the class that contains the test
     * @param args          the argument list
     * @param expectedException the expected exception or null
     */
    private void executeTest(String testName, String testClassName, String args, Class expectedException) {
        CommandLineGATK instance = new CommandLineGATK();
        String[] command = Utils.escapeExpressions(args);
        // run the executable
        boolean gotAnException = false;
        try {
            final String now = new SimpleDateFormat("HH:mm:ss").format(new Date());

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    private void performBAMListFileUnpackingTest( File tempListFile, List<SAMReaderID> expectedUnpackedFileList ) throws Exception {
        List<String> bamFiles = new ArrayList<String>();
        bamFiles.add(tempListFile.getAbsolutePath());


        CommandLineGATK testInstance = new CommandLineGATK();
        testInstance.setParser(new ParsingEngine(testInstance));


        List<SAMReaderID> unpackedBAMFileList = ListFileUtils.unpackBAMFileList(bamFiles,new ParsingEngine(testInstance));


        Assert.assertEquals(unpackedBAMFileList.size(), expectedUnpackedFileList.size(),
                            "Unpacked BAM file list contains extraneous lines");

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     * Create an instance of the GATK parsing engine, for argument processing with GATKDoclet
     *
     * @return
     */
    private ParsingEngine createStandardGATKParsingEngine() {
        CommandLineProgram clp = new CommandLineGATK();
        try {
            CommandLineProgram.start(clp, new String[]{}, true);
            return clp.parser;
        } catch (Exception e) {
            throw new RuntimeException(e);

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Related Classes of org.broadinstitute.gatk.engine.CommandLineGATK

org.broadinstitute.gatk.engine.refdata.tracks.FeatureManager

org.broadinstitute.gatk.engine.walkers.WalkerTest

org.broadinstitute.gatk.utils.help.GenericDocumentationHandler

org.broadinstitute.gatk.utils.text.ListFileUtilsUnitTest

org.broadinstitute.gatk.utils.exceptions.UserException

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Examples of org.broadinstitute.gatk.engine.CommandLineGATK

Info for general users

Info for developers

Related Classes of org.broadinstitute.gatk.engine.CommandLineGATK