96241c6637779cf843ce99ad1f02fb1c22e6dea8,java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java,DepthOfCoverageB36IntegrationTest,testMapQ0Only,#,52

Before Change


    public void testMapQ0Only() {
        // our base file
        File baseOutputFile = this.createTempFile("depthofcoveragemapq0",".tmp");
        this.setOutputFileLocation(baseOutputFile);

        String[] intervals = {"1:10,000,000-10,002,000","1:10,003,000-10,004,000"};
        String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam"};

After Change


        // our base file
        File baseOutputFile = this.createTempFile("depthofcoveragemapq0",".tmp");

        spec.setOutputFileLocation(baseOutputFile);
        spec.addAuxFile("f39af6ad99520fd4fb27b409ab0344a0",baseOutputFile);
        spec.addAuxFile("6b15f5330414b6d4e2f6caea42139fa1", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts"));
        spec.addAuxFile("cc6640d82077991dde8a2b523935cdff", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions"));