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-Added VariantFiltration integration tests 

-Added integration test for GLFs



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2133 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-11-24 02:36:27 +00:00
parent be6a549e7b
commit ee5093d2c6
3 changed files with 62 additions and 2 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
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@ -177,8 +177,6 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
filter();
}
out.printf("Processed %d loci.\n", result);
if ( writer != null )
writer.close();
}

54
java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java 100755
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@ -0,0 +1,54 @@
package org.broadinstitute.sting.gatk.walkers.filters;
import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;
import java.util.Arrays;
public class VariantFiltrationIntegrationTest extends WalkerTest {
public static String baseTestString() {
return "-T VariantFiltration -o %s -R /broad/1KG/reference/human_b36_both.fasta";
}
@Test
public void testNoAction() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("2408d449fbe7bf74099cc53d2d97c248"));
executeTest("test no action", spec);
}
@Test
public void testClusteredSnps() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -window 10 -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("58a2d4cd3d3ba1460833b45b9b8455c2"));
executeTest("test clustered SNPs", spec);
}
@Test
public void testMask() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -mask foo -B mask,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("9fc2cb210b3595159f34ddfba5a2e572"));
executeTest("test mask", spec);
}
@Test
public void testFilter1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("5effa4b4fdd4dd33a373561637a5d86e"));
executeTest("test filter #1", spec);
}
@Test
public void testFilter2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("5e0077148eda3b4274fbef1048902d47"));
executeTest("test filter #2", spec);
}
}

8
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -101,6 +101,14 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
executeTest("testSingleSamplePilot2 - Joint Estimate", spec);
}
@Test
public void testGLF() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,050,000 -bm empirical -gm JOINT_ESTIMATE -confidence 10", 1,
Arrays.asList("c552f3adcad91ee5f3ce42c204026a68"));
executeTest("testGLF", spec);
}
// --------------------------------------------------------------------------------------------------------------
//
// testing calls with SLX, 454, and SOLID data