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Integration test for BTT calculator 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1876 348d0f76-0448-11de-a6fe-93d51630548a
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chartl 2009-10-19 18:21:55 +00:00
parent cfa86d52c2
commit 10bde9e77b
1 changed files with 28 additions and 0 deletions
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java/test/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaIntegrationTest.java 100644
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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);
}
}