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UnifiedGenotyper performance tests (WG, WEx); currently takes just over an hour. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3148 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-04-09 19:42:29 +00:00
parent 0cc6d0fbbb
commit fa01876255
1 changed files with 35 additions and 0 deletions
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35
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java 100755
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package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;
import java.util.ArrayList;
public class UnifiedGenotyperPerformanceTest extends WalkerTest {
@Test
public void testUnifiedGenotyperWholeGenome() {
WalkerTestSpec spec = new WalkerTestSpec(
"-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
" -T UnifiedGenotyper" +
" -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
" -L chr1:1-50,000,000" +
" -varout /dev/null",
0,
new ArrayList(0));
executeTest("testUnifiedGenotyperWholeGenome", spec);
}
@Test
public void testUnifiedGenotyperWholeExome() {
WalkerTestSpec spec = new WalkerTestSpec(
"-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
" -T UnifiedGenotyper" +
" -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" +
" -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" +
" -varout /dev/null",
0,
new ArrayList(0));
executeTest("testUnifiedGenotyperWholeExome", spec);
}
}