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Fixing path to dbSNP file as the other one was replaced

This commit is contained in:
Eric Banks 2011-08-04 12:36:24 -04:00
parent a831af1166
commit f10588420c
2 changed files with 6 additions and 6 deletions
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2
public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
View File

@ -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 " + GATKDataLocation + "dbsnp_129_b36.vcf -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

@ -30,7 +30,7 @@ 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 " + GATKDataLocation + "dbsnp_129_b36.vcf" +
" -T CountCovariates" +
" -I " + bam +
( bam.equals( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" )
@ -97,7 +97,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
" -standard" +
" -OQ" +
" -recalFile %s" +
" -B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf",
" -B:dbsnp,VCF " + GATKDataLocation + "dbsnp_129_b36.vcf",
1, // just one output file
Arrays.asList(md5));
executeTest("testCountCovariatesUseOriginalQuals", spec);
@ -144,7 +144,7 @@ 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 " + GATKDataLocation + "dbsnp_129_b36.vcf" +
" -T CountCovariates" +
" -I " + bam +
" -standard" +
@ -249,7 +249,7 @@ 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 " + GATKDataLocation + "dbsnp_129_b36.vcf" +
" -L 1:10,000,000-10,200,000" +
" -cov ReadGroupCovariate" +
" -cov QualityScoreCovariate" +
@ -275,7 +275,7 @@ 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 " + GATKDataLocation + "dbsnp_129_b36.vcf" +
" -T CountCovariates" +
" -I " + bam +
" -cov ReadGroupCovariate" +