List of execAndCheck() Examples

Examples of execAndCheck()

org.broadinstitute.gatk.utils.runtime.ProcessController.execAndCheck()
Executes a command line program with the settings and waits for it to return, processing the output on a background thread. Throws an IOException if the ProcessOutput exit code is nonzero @param settings Settings to be run.

Examples of org.broadinstitute.gatk.utils.runtime.ProcessController.execAndCheck()

    @Test(dataProvider = "ExtensionsTest")
    public void testExtensions(final CatVariantsTestProvider cfg) throws IOException {


        ProcessController pc = ProcessController.getThreadLocal();
        ProcessSettings ps = new ProcessSettings(cfg.getCmdLine().split("\\s+"));
        pc.execAndCheck(ps);


        MD5DB.MD5Match result = md5db.testFileMD5("testExtensions", "CatVariantsTestProvider", cfg.outputFile, cfg.md5, false);
        if(result.failed) {
            final MD5Mismatch failure = new MD5Mismatch(result.actualMD5, result.expectedMD5, result.diffEngineOutput);
            Assert.fail(failure.toString());

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Examples of org.broadinstitute.gatk.utils.runtime.ProcessController.execAndCheck()

                CatVariantsVcf2,
                BaseTest.createTempFile("CatVariantsTest", ".bcf"));


        ProcessController pc = ProcessController.getThreadLocal();
        ProcessSettings ps = new ProcessSettings(cmdLine.split("\\s+"));
        pc.execAndCheck(ps);
    }


    @Test(expectedExceptions = IOException.class)
    public void testMismatchedExtensions2() throws IOException {

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Examples of org.broadinstitute.gatk.utils.runtime.ProcessController.execAndCheck()

                CatVariantsBcf2,
                BaseTest.createTempFile("CatVariantsTest", ".vcf"));


        ProcessController pc = ProcessController.getThreadLocal();
        ProcessSettings ps = new ProcessSettings(cmdLine.split("\\s+"));
        pc.execAndCheck(ps);
    }
}

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