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added integration test for intervals with no coverage due to filtering 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3414 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-05-21 16:52:42 +00:00
parent 7fb3f2d3eb
commit 745d7c582f
1 changed files with 17 additions and 0 deletions
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17
java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java
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@ -80,6 +80,23 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
execute("testBaseOutputNoFiltering",spec);
}
@Test
public void testNoCoverageDueToFiltering() {
File baseOutputFile = this.createTempFile("depthofcoveragenofiltering",".tmp");
this.setOutputFileLocation(baseOutputFile);
String[] intervals = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/fhs_jhs_30_targts.interval_list"};
String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/FHS_indexed_subset.bam"};
String cmd = buildRootCmd(hg18,new ArrayList<String>(Arrays.asList(bams)),new ArrayList<String>(Arrays.asList(intervals))) + " -mmq 0 -mbq 5 --maxBaseQuality 4 -dels -baseCounts -pt readgroup -pt sample -pt library --outputFormat csv";
WalkerTestSpec spec = new WalkerTestSpec(cmd,0, new ArrayList<String>());
spec.addAuxFile("d570c27d82a80ebd2852e9d34aff4e87",baseOutputFile);
spec.addAuxFile("00107eea991f7379771b29dea0c859cb",createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
execute("testNoCoverageDueToFiltering",spec);
}
public File createTempFileFromBase(String name) {
File fl = new File(name);
fl.deleteOnExit();