From 10bde9e77b623c4a3185fba4f3eb36c174bee8de Mon Sep 17 00:00:00 2001 From: chartl Date: Mon, 19 Oct 2009 18:21:55 +0000 Subject: [PATCH] Integration test for BTT calculator git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1876 348d0f76-0448-11de-a6fe-93d51630548a --- ...ionTableCalculatorJavaIntegrationTest.java | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 java/test/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaIntegrationTest.java diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaIntegrationTest.java new file mode 100644 index 000000000..382262dc3 --- /dev/null +++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaIntegrationTest.java @@ -0,0 +1,28 @@ +package org.broadinstitute.sting.playground.gatk.walkers; + +import org.junit.Test; +import org.broadinstitute.sting.WalkerTest; + +import java.util.Arrays; + +/** + * Created by IntelliJ IDEA. + * User: chartl + * Date: Oct 19, 2009 + * Time: 1:57:59 PM + * To change this template use File | Settings | File Templates. + */ +public class BaseTransitionTableCalculatorJavaIntegrationTest extends WalkerTest{ + + public static final String OUTPUT_MD5 = "856a3124fb078b4d820f935369ec53cc"; + public static final String LOCUS = "1:10,000,000-10,200,000"; + public static final String BAM_FILE = "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam"; + public static final String REFERENCE = "/broad/1KG/reference/human_b36_both.fasta"; + + @Test + public void testBaseTransitionTableCalculatorJava() { + String args = "-T BaseTransitionTableCalculatorJava -o %s -I "+BAM_FILE+" -L "+LOCUS+" -R "+REFERENCE; + WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(args,1,Arrays.asList(OUTPUT_MD5)); + executeTest("testBaseTransitionTableCalculatorJava", spec); + } +}