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Initial HLA Caller integration tests. Kind of painful, but will improve with code refactoring. 

This baby is now officially ours.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3593 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2010-06-18 20:35:27 +00:00
parent f44d8b150f
commit 1e06d2bf68
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java/test/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/HLACallerIntegrationTest.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.HLAcaller;
import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;
import java.util.Arrays;
public class HLACallerIntegrationTest extends WalkerTest {
private static final String intervals = validationDataLocation + "HLA_EXONS.intervals";
@Test
public void testFindClosestHLA() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T FindClosestHLA -I " + validationDataLocation + "NA12878.HISEQ.HLA.bam -R " + oneKGLocation + "reference/human_b36_both.fasta -L " + intervals + " -useInterval " + intervals + " -HLAdictionary " + validationDataLocation + "HLA_DICTIONARY.txt -PolymorphicSites " + validationDataLocation + "HLA_POLYMORPHIC_SITES.txt -o %s", 1,
Arrays.asList("a49b6f54a4585d1dd958c55a5523427d"));
executeTest("test FindClosestHLA", spec);
}
@Test
public void testCalculateBaseLikelihoods() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T CalculateBaseLikelihoods -I " + validationDataLocation + "NA12878.HISEQ.HLA.bam -R " + oneKGLocation + "reference/human_b36_both.fasta -L " + intervals + " -filter " + validationDataLocation + "HLA_HISEQ.filter -maxAllowedMismatches 6 -minRequiredMatches 0 -o %s", 1,
Arrays.asList("3272e3db32a3370b728457cd9a071339"));
executeTest("test CalculateBaseLikelihoods", spec);
}
@Test
public void testHLACaller() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T HLACaller -noVerbose -I " + validationDataLocation + "NA12878.HISEQ.HLA.bam -R " + oneKGLocation + "reference/human_b36_both.fasta -L " + intervals + " -useInterval " + intervals + " -HLAdictionary " + validationDataLocation + "HLA_DICTIONARY.txt -filter " + validationDataLocation + "HLA_HISEQ.filter -maxAllowedMismatches 6 -minRequiredMatches 5 -HLAfrequencies " + validationDataLocation + "HLA_FREQUENCIES.txt -bl " + validationDataLocation + "HLA_HISEQ.baselikelihoods -o %s", 1,
Arrays.asList("f9931b378bde213e71fca6ecaa24b48b"));
executeTest("test HLACaller", spec);
}
}