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VCF3 now dynamically determined

This commit is contained in:
Mark DePristo 2011-08-08 15:05:47 -04:00
parent ba7353c561
commit 4f8fc0f2f1
3 changed files with 8 additions and 8 deletions
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4
public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
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@ -236,7 +236,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference + "-R " + b36KGReference +
" -B:dbsnp,VCF3 " + validationDataLocation + "vcfexample3.vcf" + " -B:dbsnp " + validationDataLocation + "vcfexample3.vcf" +
" -T CountCovariates" + " -T CountCovariates" +
" -I " + bam + " -I " + bam +
" -L 1:10,000,000-10,200,000" + " -L 1:10,000,000-10,200,000" +
@ -284,7 +284,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference + "-R " + b36KGReference +
" -B:anyNameABCD,VCF3 " + validationDataLocation + "vcfexample3.vcf" + " -B:anyNameABCD " + validationDataLocation + "vcfexample3.vcf" +
" -T CountCovariates" + " -T CountCovariates" +
" -I " + bam + " -I " + bam +
" -B:dbsnp,vcf " + b36dbSNP129 + " -B:dbsnp,vcf " + b36dbSNP129 +

8
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
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@ -233,8 +233,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
String extraArgs = "-L 1:1-10,000,000"; String extraArgs = "-L 1:1-10,000,000";
String tests = cmdRoot + String tests = cmdRoot +
" -B:dbsnp " + b36dbSNP129 + " -B:dbsnp " + b36dbSNP129 +
" -B:eval,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" + " -B:eval " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
" -B:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf"; " -B:comp_genotypes " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s", WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
1, Arrays.asList("14054badcd89b24c2375e1d09918f681")); 1, Arrays.asList("14054badcd89b24c2375e1d09918f681"));
executeTestParallel("testSelect1", spec); executeTestParallel("testSelect1", spec);
@ -244,7 +244,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
public void testVEGenotypeConcordance() { public void testVEGenotypeConcordance() {
String vcfFile = "GenotypeConcordanceEval.vcf"; String vcfFile = "GenotypeConcordanceEval.vcf";
WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -ST CpG -B:eval,VCF3 " + validationDataLocation + vcfFile + " -B:comp,VCF3 " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s", WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -ST CpG -B:eval " + validationDataLocation + vcfFile + " -B:comp " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s",
1, 1,
Arrays.asList("96f27163f16bb945f19c6623cd6db34e")); Arrays.asList("96f27163f16bb945f19c6623cd6db34e"));
executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec); executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec);
@ -252,7 +252,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test @Test
public void testCompVsEvalAC() { public void testCompVsEvalAC() {
String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance -B:evalYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf"; String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance -B:evalYRI " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("d1932be3748fcf6da77dc51aec323710")); WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("d1932be3748fcf6da77dc51aec323710"));
executeTestParallel("testCompVsEvalAC",spec); executeTestParallel("testCompVsEvalAC",spec);
} }

4
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
View File

@ -16,7 +16,7 @@ public class VariantContextIntegrationTest extends WalkerTest {
private static String root = cmdRoot + private static String root = cmdRoot +
" -L 1:1-1,000,000 -B:dbsnp,vcf " + b36dbSNP129 + " -L 1:1-1,000,000 -B:dbsnp,vcf " + b36dbSNP129 +
" -B:vcf,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf"; " -B:vcf " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf";
private static final class VCITTest extends TestDataProvider { private static final class VCITTest extends TestDataProvider {
String args, md5; String args, md5;
@ -58,7 +58,7 @@ public class VariantContextIntegrationTest extends WalkerTest {
public void testToVCF() { public void testToVCF() {
// this really just tests that we are seeing the same number of objects over all of chr1 // this really just tests that we are seeing the same number of objects over all of chr1
WalkerTestSpec spec = new WalkerTestSpec( cmdRoot + " -NO_HEADER -B:vcf,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -L 1:1-1000000 -o %s --outputVCF %s", WalkerTestSpec spec = new WalkerTestSpec( cmdRoot + " -NO_HEADER -B:vcf " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -L 1:1-1000000 -o %s --outputVCF %s",
2, // just one output file 2, // just one output file
Arrays.asList("e3c35d0c4b5d4935c84a270f9df0951f", "ff91731213fd0bbdc200ab6fd1c93e63")); Arrays.asList("e3c35d0c4b5d4935c84a270f9df0951f", "ff91731213fd0bbdc200ab6fd1c93e63"));
executeTest("testToVCF", spec); executeTest("testToVCF", spec);