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Removed redundant overrride createTempFileFromBase (same code as super class) and added some finals to DepthOfCoverageB36IntegrationTest

This commit is contained in:
Valentin Ruano-Rubio 2014-05-28 19:02:04 -04:00
parent e0c221470c
commit 938172d7f0
1 changed files with 6 additions and 12 deletions
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18
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageB36IntegrationTest.java
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@ -67,12 +67,6 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest {
} }
} }
public File createTempFileFromBase(String name) {
File fl = new File(name);
fl.deleteOnExit();
return fl;
}
@Test @Test
public void testMapQ0Only() { public void testMapQ0Only() {
String[] intervals = {"1:10,000,000-10,002,000","1:10,003,000-10,004,000"}; 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<String>()); WalkerTestSpec spec = new WalkerTestSpec(cmd,0,new ArrayList<String>());
// our base file // our base file
File baseOutputFile = this.createTempFile("depthofcoveragemapq0",".tmp"); final File baseOutputFile = createTempFile("depthofcoveragemapq0",".tmp");
spec.setOutputFileLocation(baseOutputFile); spec.setOutputFileLocation(baseOutputFile);
spec.addAuxFile("f39af6ad99520fd4fb27b409ab0344a0",baseOutputFile); spec.addAuxFile("f39af6ad99520fd4fb27b409ab0344a0",baseOutputFile);
@ -100,13 +94,13 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest {
@Test @Test
public void testLotsOfSamples() { public void testLotsOfSamples() {
String[] intervals = {"1:1105290-1105295"}; final String[] intervals = {"1:1105290-1105295"};
String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/pilot3.CEU+TSI.5loci.bam"}; final String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/pilot3.CEU+TSI.5loci.bam"};
String cmd = buildRootCmd(b36KGReference, new ArrayList<String>(Arrays.asList(bams)), new ArrayList<String>(Arrays.asList(intervals))); final String cmd = buildRootCmd(b36KGReference, new ArrayList<String>(Arrays.asList(bams)), new ArrayList<String>(Arrays.asList(intervals)));
WalkerTestSpec spec = new WalkerTestSpec(cmd,0,new ArrayList<String>()); final WalkerTestSpec spec = new WalkerTestSpec(cmd,0,new ArrayList<String>());
File baseOutputFile = this.createTempFile("testManySamples",".tmp"); final File baseOutputFile = createTempFile("testManySamples",".tmp");
spec.setOutputFileLocation(baseOutputFile); spec.setOutputFileLocation(baseOutputFile);
spec.addAuxFile("c9561b52344536d2b06ab97b0bb1a234",baseOutputFile); spec.addAuxFile("c9561b52344536d2b06ab97b0bb1a234",baseOutputFile);