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Replacing hardcoded dbsnp129 with BaseTest variable

This commit is contained in:
Mark DePristo 2011-08-03 22:15:22 -04:00
parent d0279bb28c
commit 490ca475fc
7 changed files with 13 additions and 13 deletions
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2
public/java/test/org/broadinstitute/sting/BaseTest.java
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@ -64,7 +64,7 @@ public abstract class BaseTest {
public static final String b37Refseq = refseqAnnotationLocation + "refGene-big-table-b37.txt";
public static final String dbsnpDataLocation = GATKDataLocation;
public static final String b36dbSNP129 = dbsnpDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf";
public static final String b36dbSNP129 = dbsnpDataLocation + "dbsnp_129_b36.vcf";
public static final String b37dbSNP132 = dbsnpDataLocation + "dbsnp_132_b37.vcf";
public static final String hapmapDataLocation = comparisonDataLocation + "Validated/HapMap/3.3/";

2
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
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@ -94,7 +94,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testDBTagWithDbsnp() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf -G \"Standard\" --variants:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variants", 1,
baseTestString() + " -B:dbsnp,vcf " + b36dbSNP129 + " -G \"Standard\" --variants:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variants", 1,
Arrays.asList("3da8ca2b6bdaf6e92d94a8c77a71313d"));
executeTest("getting DB tag with dbSNP", spec);
}

2
public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java
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@ -24,7 +24,7 @@ public class FastaAlternateReferenceIntegrationTest extends WalkerTest {
executeTest("testFastaReference", spec1b);
WalkerTestSpec spec2 = new WalkerTestSpec(
"-T FastaAlternateReferenceMaker -R " + b36KGReference + " -B:indels,VCF " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 --snpmask:vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf -L 1:10,075,000-10,075,380;1:10,093,447-10,093,847;1:10,271,252-10,271,452 -o %s",
"-T FastaAlternateReferenceMaker -R " + b36KGReference + " -B:indels,VCF " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 --snpmask:vcf " + b36dbSNP129 + " -L 1:10,075,000-10,075,380;1:10,093,447-10,093,847;1:10,271,252-10,271,452 -o %s",
1,
Arrays.asList("0567b32ebdc26604ddf2a390de4579ac"));
executeTest("testFastaAlternateReferenceIndels", spec2);

6
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java
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@ -15,7 +15,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
" -glm BOTH" +
" -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
" -L chr1:1-50,000,000" +
" -B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf" +
" -B:dbsnp,VCF " + b36dbSNP129 +
" -o /dev/null",
0,
new ArrayList<String>(0));
@ -30,7 +30,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
" -glm BOTH" +
" -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" +
" -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" +
" -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf" +
" -B:dbsnp,vcf " + b36dbSNP129 +
" -o /dev/null",
0,
new ArrayList<String>(0));
@ -46,7 +46,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
" -glm BOTH" +
" -L chr1:1-50,000,000" +
" -nt 10" +
" -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf" +
" -B:dbsnp,vcf " + b36dbSNP129 +
" -o /dev/null",
0,
new ArrayList<String>(0));

2
public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
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@ -17,7 +17,7 @@ public class RealignerTargetCreatorIntegrationTest extends WalkerTest {
executeTest("test standard", spec1);
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
"-T RealignerTargetCreator -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000 -o %s",
"-T RealignerTargetCreator -B:dbsnp,vcf " + b36dbSNP129 + " -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000 -o %s",
1,
Arrays.asList("0367d39a122c8ac0899fb868a82ef728"));
executeTest("test dbsnp", spec2);

10
public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
View File

@ -55,7 +55,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf" +
" -B:dbsnp,vcf " + b36dbSNP129 +
" -T CountCovariates" +
" -I " + bam +
( bam.equals( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" )
@ -136,7 +136,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
" -standard" +
" -OQ" +
" -recalFile %s" +
" -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf",
" -B:dbsnp,vcf " + b36dbSNP129,
1, // just one output file
Arrays.asList(md5));
executeTest("testCountCovariatesUseOriginalQuals", spec);
@ -183,7 +183,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf" +
" -B:dbsnp,vcf " + b36dbSNP129 +
" -T CountCovariates" +
" -I " + bam +
" -standard" +
@ -288,7 +288,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
" -B:anyNameABCD,VCF3 " + validationDataLocation + "vcfexample3.vcf" +
" -T CountCovariates" +
" -I " + bam +
" -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf" +
" -B:dbsnp,vcf " + b36dbSNP129 +
" -L 1:10,000,000-10,200,000" +
" -cov ReadGroupCovariate" +
" -cov QualityScoreCovariate" +
@ -313,7 +313,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf" +
" -B:dbsnp,vcf " +
" -T CountCovariates" +
" -I " + bam +
" -cov ReadGroupCovariate" +

2
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
View File

@ -15,7 +15,7 @@ public class VariantContextIntegrationTest extends WalkerTest {
" -R " + b36KGReference;
private static String root = cmdRoot +
" -L 1:1-1,000,000 -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf" +
" -L 1:1-1,000,000 -B:dbsnp,vcf " + b36dbSNP129 +
" -B:vcf,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf";
private static final class VCITTest extends TestDataProvider {