From 9d263b2565289ffd20998b63bf89a641a2acdeb1 Mon Sep 17 00:00:00 2001 From: depristo Date: Mon, 28 Dec 2009 23:57:25 +0000 Subject: [PATCH] Integration tests for count duplicates walker validated on a TCGA hybrid capture lane. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2459 348d0f76-0448-11de-a6fe-93d51630548a --- .../DuplicatesWalkersIntegrationTest.java | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100755 java/test/org/broadinstitute/sting/playground/gatk/walkers/duplicates/DuplicatesWalkersIntegrationTest.java diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/duplicates/DuplicatesWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/duplicates/DuplicatesWalkersIntegrationTest.java new file mode 100755 index 000000000..660dfd079 --- /dev/null +++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/duplicates/DuplicatesWalkersIntegrationTest.java @@ -0,0 +1,25 @@ +package org.broadinstitute.sting.playground.gatk.walkers.duplicates; + +import org.broadinstitute.sting.WalkerTest; +import org.junit.Test; + +import java.io.File; +import java.util.Arrays; +import java.util.List; + +public class DuplicatesWalkersIntegrationTest extends WalkerTest { + public void testClipper(String name, String args, String md5) { + WalkerTestSpec spec = new WalkerTestSpec( + "-T CountDuplicates " + + "-R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta " + + "-I /humgen/gsa-hpprojects/GATK/data/Validation_Data/TCGA-06-0188.aligned.duplicates_marked.bam " + + "-o %s " + args, + 1, // just one output file + Arrays.asList("tmp"), + Arrays.asList(md5)); + List result = executeTest(name, spec).getFirst(); + } + + @Test public void testChr110Mb() { testClipper("testChr1-10mb", "-L chr1:1-10,000,000 --quiet", ""); } + @Test public void testIntervalVerbose() { testClipper("testIntervalVerbose", "-L chr1:6,527,154-6,528,292", ""); } +} \ No newline at end of file