zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Adding performance tests for the indel realigner; should take ~3 hours. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3151 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-04-11 04:45:22 +00:00
parent 3434a61146
commit d06c7835d8
4 changed files with 86 additions and 6 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java
View File

@ -16,7 +16,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
" -L chr1:1-50,000,000" +
" -varout /dev/null",
0,
new ArrayList(0));
new ArrayList<String>(0));
executeTest("testUnifiedGenotyperWholeGenome", spec);
}
@ -29,7 +29,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
" -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" +
" -varout /dev/null",
0,
new ArrayList(0));
new ArrayList<String>(0));
executeTest("testUnifiedGenotyperWholeExome", spec);
}
}

46
java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java 100755
View File

@ -0,0 +1,46 @@
package org.broadinstitute.sting.gatk.walkers.indels;
import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;
import java.util.ArrayList;
public class IndelRealignerPerformanceTest extends WalkerTest {
@Test
public void testRealigner() {
WalkerTestSpec spec1 = new WalkerTestSpec(
"-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
" -T IndelRealigner" +
" -LOD 5" +
" -maxConsensuses 100" +
" -greedy 100" +
" -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod" +
" -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
" -L chr1:1-5,650,000" +
" -compress 1" +
" -sort NO_SORT" +
" -targetIntervals " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.realigner.intervals" +
" -O /dev/null",
0,
new ArrayList<String>(0));
executeTest("testRealignerTargetCreatorWholeGenome", spec1);
WalkerTestSpec spec2 = new WalkerTestSpec(
"-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
" -T IndelRealigner" +
" -LOD 5" +
" -maxConsensuses 100" +
" -greedy 100" +
" -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod" +
" -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" +
" -L chr1:1-150,000,000" +
" -compress 1" +
" -sort NO_SORT" +
" -targetIntervals " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.realigner.intervals" +
" -O /dev/null",
0,
new ArrayList<String>(0));
executeTest("testRealignerTargetCreatorWholeExome", spec2);
}
}

34
java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorPerformanceTest.java 100755
View File

@ -0,0 +1,34 @@
package org.broadinstitute.sting.gatk.walkers.indels;
import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;
import java.util.ArrayList;
public class RealignerTargetCreatorPerformanceTest extends WalkerTest {
@Test
public void testRealignerTargetCreator() {
WalkerTestSpec spec1 = new WalkerTestSpec(
"-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
" -T RealignerTargetCreator" +
" -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod" +
" -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
" -L chr1:1-50,000,000" +
" -o /dev/null",
0,
new ArrayList<String>(0));
executeTest("testRealignerTargetCreatorWholeGenome", spec1);
WalkerTestSpec spec2 = new WalkerTestSpec(
"-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
" -T RealignerTargetCreator" +
" -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod" +
" -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" +
" -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" +
" -o /dev/null",
0,
new ArrayList<String>(0));
executeTest("testRealignerTargetCreatorWholeExome", spec2);
}
}

8
java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
View File

@ -18,7 +18,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
" -OQ" +
" -recalFile /dev/null",
0,
new ArrayList(0));
new ArrayList<String>(0));
executeTest("testCountCovariatesWholeGenome", spec);
}
@ -33,7 +33,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
" -OQ" +
" -recalFile /dev/null",
0,
new ArrayList(0));
new ArrayList<String>(0));
executeTest("testCountCovariatesWholeExome", spec);
}
@ -48,7 +48,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
" -recalFile " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.recal.csv" +
" -outputBam /dev/null",
0,
new ArrayList(0));
new ArrayList<String>(0));
executeTest("testTableRecalibratorWholeGenome", spec);
}
@ -63,7 +63,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
" -recalFile " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.recal.csv" +
" -outputBam /dev/null",
0,
new ArrayList(0));
new ArrayList<String>(0));
executeTest("testTableRecalibratorWholeExome", spec);
}
}