From f1d1252be287d1167ba2bfb3a9574b1f6dec7f01 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Thu, 11 Aug 2011 17:04:09 -0400
Subject: [PATCH] Fixing syntax of BQSR and UG performance tests.

---
 public/java/test/org/broadinstitute/sting/BaseTest.java     | 1 +
 .../walkers/genotyper/UnifiedGenotyperPerformanceTest.java  | 6 +++---
 .../recalibration/RecalibrationWalkersPerformanceTest.java  | 4 ++--
 3 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/public/java/test/org/broadinstitute/sting/BaseTest.java b/public/java/test/org/broadinstitute/sting/BaseTest.java
index 7a749c0a2..63faf1ab9 100755
--- a/public/java/test/org/broadinstitute/sting/BaseTest.java
+++ b/public/java/test/org/broadinstitute/sting/BaseTest.java
@@ -67,6 +67,7 @@ public abstract class BaseTest {
     public static final String b36dbSNP129 = dbsnpDataLocation + "dbsnp_129_b36.vcf";
     public static final String b37dbSNP129 = dbsnpDataLocation + "dbsnp_129_b37.vcf";
     public static final String b37dbSNP132 = dbsnpDataLocation + "dbsnp_132_b37.vcf";
+    public static final String hg18dbSNP132 = dbsnpDataLocation + "dbsnp_132.hg18.vcf";
 
     public static final String hapmapDataLocation = comparisonDataLocation + "Validated/HapMap/3.3/";
     public static final String b37hapmapGenotypes = hapmapDataLocation + "genotypes_r27_nr.b37_fwd.vcf";
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java
index fb7e84d22..3ff453dab 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java
@@ -15,7 +15,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
                         " -glm BOTH" +
                         " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
                         " -L chr1:1-50,000,000" +
-                        " --dbsnp:VCF " + b36dbSNP129 +
+                        " --dbsnp:VCF " + hg18dbSNP132 +
                         " -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" +
-                        " --dbsnp:vcf " + b36dbSNP129 +
+                        " --dbsnp:vcf " + hg18dbSNP132 +
                         " -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" +
-                        " --dbsnp:vcf " + b36dbSNP129 +
+                        " --dbsnp:vcf " + hg18dbSNP132 +
                         " -o /dev/null",
                 0,
                 new ArrayList<String>(0));
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
index 43ea401f7..bccb95795 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
@@ -16,7 +16,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
                         " -L chr1:1-50,000,000" +
                         " -standard" +
                         " -OQ" +
-                        " -B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
+                        " -knownSites " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
                         " -recalFile /dev/null" + moreArgs,
                 0,
                 new ArrayList<String>(0));
@@ -31,7 +31,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
                         " -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" +
                         " -standard" +
                         " -OQ" +
-                        " -B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
+                        " -knownSites " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
                         " -recalFile /dev/null" + moreArgs,
                 0,
                 new ArrayList<String>(0));