Package org.broadinstitute.gatk.utils.runtime

Examples of org.broadinstitute.gatk.utils.runtime.ProcessSettings

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    @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);
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                CatVariantsVcf1,
                CatVariantsVcf2,
                BaseTest.createTempFile("CatVariantsTest", ".bcf"));

        ProcessController pc = ProcessController.getThreadLocal();
        ProcessSettings ps = new ProcessSettings(cmdLine.split("\\s+"));
        pc.execAndCheck(ps);
    }
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                CatVariantsVcf1,
                CatVariantsBcf2,
                BaseTest.createTempFile("CatVariantsTest", ".vcf"));

        ProcessController pc = ProcessController.getThreadLocal();
        ProcessSettings ps = new ProcessSettings(cmdLine.split("\\s+"));
        pc.execAndCheck(ps);
    }
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            cmd[i++] = "-e";
            cmd[i++] = expression.toString();
            for (String arg: this.args)
                cmd[i++] = arg;

            ProcessSettings processSettings = new ProcessSettings(cmd);
            if (logger.isDebugEnabled()) {
                processSettings.getStdoutSettings().printStandard(true);
                processSettings.getStderrSettings().printStandard(true);
            }

            ProcessController controller = ProcessController.getThreadLocal();

            if (logger.isDebugEnabled()) {
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Related Classes of org.broadinstitute.gatk.utils.runtime.ProcessSettings

  • org.broadinstitute.gatk.tools.CatVariantsIntegrationTest
  • org.broadinstitute.gatk.utils.R.RScriptExecutor
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