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Add an integration test for Beagle (one for ProduceBeagleInput and one for BeagleOutputToVCFWalker) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3897 348d0f76-0448-11de-a6fe-93d51630548a
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delangel 2010-07-29 18:49:22 +00:00
parent 4d4cf6e1dc
commit 5af986e0c1
1 changed files with 57 additions and 0 deletions
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java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java 100755
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/*
* Copyright (c) 2010.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.gatk.walkers;
import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;
import java.util.Arrays;
public class BeagleIntegrationTest extends WalkerTest {
private static final String beagleValidationDataLocation = validationDataLocation + "/Beagle/";
@Test
public void testBeagleOutput() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T BeagleOutputToVCF -R " + oneKGLocation + "reference/human_g1k_v37.fasta " +
"-B variant,VCF," + beagleValidationDataLocation + "inttestbgl.input.vcf " +
"-B beagleR2,BEAGLE," + beagleValidationDataLocation + "inttestbgl.r2 " +
"-B beagleProbs,BEAGLE," + beagleValidationDataLocation + "inttestbgl.gprobs " +
"-B beaglePhased,BEAGLE," + beagleValidationDataLocation + "inttestbgl.phased " +
"-output %s", 1, Arrays.asList("e7b9aac20246f26ffcc599850f6cb2a0"));
executeTest("test BeagleOutputToVCF", spec);
}
@Test
public void testBeagleInput() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T ProduceBeagleInput -R " + oneKGLocation + "reference/human_g1k_v37.fasta " +
"-B variant,VCF," + beagleValidationDataLocation + "inttestbgl.input.vcf " +
"-beagle %s", 1, Arrays.asList("c0d30e5dbe903874f8422a0e63a5118e"));
executeTest("test BeagleInput", spec);
}
}