From f10588420c11e8db007a2c975e61206e68a71299 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 4 Aug 2011 12:36:24 -0400
Subject: [PATCH] Fixing path to dbSNP file as the other one was replaced

---
 .../indels/RealignerTargetCreatorIntegrationTest.java  |  2 +-
 .../RecalibrationWalkersIntegrationTest.java           | 10 +++++-----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
index f5ed69476..60312dbd2 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
@@ -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);
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
index 049f44845..e81d2670c 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
@@ -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" +