diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageB36IntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageB36IntegrationTest.java index af74beec6..447515d0e 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageB36IntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageB36IntegrationTest.java @@ -67,12 +67,6 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest { } } - public File createTempFileFromBase(String name) { - File fl = new File(name); - fl.deleteOnExit(); - return fl; - } - @Test public void testMapQ0Only() { String[] intervals = {"1:10,000,000-10,002,000","1:10,003,000-10,004,000"}; @@ -83,7 +77,7 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec(cmd,0,new ArrayList()); // our base file - File baseOutputFile = this.createTempFile("depthofcoveragemapq0",".tmp"); + final File baseOutputFile = createTempFile("depthofcoveragemapq0",".tmp"); spec.setOutputFileLocation(baseOutputFile); spec.addAuxFile("f39af6ad99520fd4fb27b409ab0344a0",baseOutputFile); @@ -100,13 +94,13 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest { @Test public void testLotsOfSamples() { - String[] intervals = {"1:1105290-1105295"}; - String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/pilot3.CEU+TSI.5loci.bam"}; - String cmd = buildRootCmd(b36KGReference, new ArrayList(Arrays.asList(bams)), new ArrayList(Arrays.asList(intervals))); + final String[] intervals = {"1:1105290-1105295"}; + final String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/pilot3.CEU+TSI.5loci.bam"}; + final String cmd = buildRootCmd(b36KGReference, new ArrayList(Arrays.asList(bams)), new ArrayList(Arrays.asList(intervals))); - WalkerTestSpec spec = new WalkerTestSpec(cmd,0,new ArrayList()); + final WalkerTestSpec spec = new WalkerTestSpec(cmd,0,new ArrayList()); - File baseOutputFile = this.createTempFile("testManySamples",".tmp"); + final File baseOutputFile = createTempFile("testManySamples",".tmp"); spec.setOutputFileLocation(baseOutputFile); spec.addAuxFile("c9561b52344536d2b06ab97b0bb1a234",baseOutputFile);