From 7ef87e51260bb20e258db7e6b64aab88096fab61 Mon Sep 17 00:00:00 2001 From: hanna Date: Thu, 13 May 2010 15:40:43 +0000 Subject: [PATCH] An integration test based on validating pileup to test parallelism in reads, reference, and RODs. This test runs in less than a minute and fell over instantly in the case of the Tribble parallelism issue. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3358 348d0f76-0448-11de-a6fe-93d51630548a --- .../qc/ValidatingPileupIntegrationTest.java | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 java/test/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupIntegrationTest.java diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupIntegrationTest.java new file mode 100644 index 000000000..72e03346e --- /dev/null +++ b/java/test/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupIntegrationTest.java @@ -0,0 +1,25 @@ +package org.broadinstitute.sting.gatk.walkers.qc; + +import org.junit.Test; +import org.broadinstitute.sting.WalkerTest; + +import java.util.Collections; + +/** + * Run validating pileup across a set of core data as proof of the integrity of the GATK core. + * + * @author mhanna + * @version 0.1 + */ +public class ValidatingPileupIntegrationTest extends WalkerTest { + @Test + public void testEcoliThreaded() { + WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( + "-T ValidatingPileup" + + " -I /humgen/gsa-scr1/GATK_Data/Validation_Data/MV1994.selected.bam" + + " -R /humgen/gsa-scr1/GATK_Data/Validation_Data/Escherichia_coli_K12_MG1655.fasta" + + " -B pileup,SAMPileup,/humgen/gsa-scr1/GATK_Data/Validation_Data/MV1994.selected.pileup" + + " -S SILENT -nt 8",0, Collections.emptyList()); + executeTest("testEcoliThreaded",spec); + } +}