From 745d7c582f464e762f30131ae411f36f1ce61986 Mon Sep 17 00:00:00 2001 From: chartl Date: Fri, 21 May 2010 16:52:42 +0000 Subject: [PATCH] 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 --- .../DepthOfCoverageIntegrationTest.java | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java index 7dae9ee8d..b6f4d13d0 100644 --- a/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java @@ -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(Arrays.asList(bams)),new ArrayList(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()); + + 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();