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Adding performance tests for the recalibrator (Whole Genome and Whole Exome tests). 

Should take ~3 hours to run.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3145 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-04-09 18:30:59 +00:00
parent e73e6a4fb0
commit 71f38a9199
2 changed files with 70 additions and 0 deletions
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1
java/test/org/broadinstitute/sting/BaseTest.java
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@ -44,6 +44,7 @@ public abstract class BaseTest {
protected static String oneKGLocation = "/broad/1KG/";
protected static String GATKDataLocation = "/humgen/gsa-hpprojects/GATK/data/";
protected static String validationDataLocation = GATKDataLocation + "Validation_Data/";
protected static String evaluationDataLocation = GATKDataLocation + "Evaluation_Data/";
protected static String testDir = "testdata/";
protected static boolean alreadySetup = false;

69
java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java 100755
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@ -0,0 +1,69 @@
package org.broadinstitute.sting.gatk.walkers.recalibration;
import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;
import java.util.ArrayList;
public class RecalibrationWalkersPerformanceTest extends WalkerTest {
@Test
public void testCountCovariatesWholeGenome() {
WalkerTestSpec spec = new WalkerTestSpec(
"-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
" -T CountCovariates" +
" -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
" -L chr1:1-50,000,000" +
" -standard" +
" -OQ" +
" -recalFile /dev/null",
0,
new ArrayList(0));
executeTest("testCountCovariatesWholeGenome", spec);
}
@Test
public void testCountCovariatesWholeExome() {
WalkerTestSpec spec = new WalkerTestSpec(
"-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
" -T CountCovariates" +
" -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" +
" -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" +
" -standard" +
" -OQ" +
" -recalFile /dev/null",
0,
new ArrayList(0));
executeTest("testCountCovariatesWholeExome", spec);
}
@Test
public void testTableRecalibratorWholeGenome() {
WalkerTestSpec spec = new WalkerTestSpec(
"-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
" -T TableRecalibration" +
" -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
" -L chr1:1-50,000,000" +
" -OQ" +
" -recalFile " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.recal.csv" +
" -outputBam /dev/null",
0,
new ArrayList(0));
executeTest("testTableRecalibratorWholeGenome", spec);
}
@Test
public void testTableRecalibratorWholeExome() {
WalkerTestSpec spec = new WalkerTestSpec(
"-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
" -T TableRecalibration" +
" -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" +
" -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" +
" -OQ" +
" -recalFile " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.recal.csv" +
" -outputBam /dev/null",
0,
new ArrayList(0));
executeTest("testTableRecalibratorWholeExome", spec);
}
}