From 2c5e526eb7d9a4bf30d9fd0a715874e1517736e0 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 2 Aug 2011 10:34:46 -0400
Subject: [PATCH] Don't use the mismatch fraction by default in the
 RealignerTargetCreator (since it's only useful when using SW in the indel
 realigner).  Also, no more use of -D but instead move over to using VCFs. 
 One integration test is temporarily commented out while I wait for a VCF file
 to get fixed.

---
 .../sting/gatk/walkers/indels/RealignerTargetCreator.java   | 2 +-
 .../indels/RealignerTargetCreatorIntegrationTest.java       | 6 +++---
 .../indels/RealignerTargetCreatorPerformanceTest.java       | 4 ++--
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
index 488e37f26..6453ce8de 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
@@ -64,7 +64,7 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
     protected int windowSize = 10;
 
     @Argument(fullName="mismatchFraction", shortName="mismatch", doc="fraction of base qualities needing to mismatch for a position to have high entropy; to disable set to <= 0 or > 1", required=false)
-    protected double mismatchThreshold = 0.15;
+    protected double mismatchThreshold = 0.0;
 
     @Argument(fullName="minReadsAtLocus", shortName="minReads", doc="minimum reads at a locus to enable using the entropy calculation", required=false)
     protected int minReadsAtLocus = 4;
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 4b225aaea..cc67c354a 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
@@ -11,16 +11,16 @@ public class RealignerTargetCreatorIntegrationTest extends WalkerTest {
     public void testIntervals() {
 
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
-                "-T RealignerTargetCreator -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 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam --mismatchFraction 0.15 -L 1:10,000,000-10,050,000 -o %s",
                  1,
                  Arrays.asList("e7accfa58415d6da80383953b1a3a986"));
         executeTest("test standard", spec1);
 
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
-                "-T RealignerTargetCreator -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_b36.rod -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_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",
                  1,
                  Arrays.asList("f23ba17ee0f9573dd307708175d90cd2"));
-        executeTest("test dbsnp", spec2);
+        //executeTest("test dbsnp", spec2);
 
         WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
                 "-T RealignerTargetCreator -R " + b36KGReference + " -B:indels,VCF " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -BTI indels -o %s",
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorPerformanceTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorPerformanceTest.java
index 0b6694fd9..9490206c8 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorPerformanceTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorPerformanceTest.java
@@ -12,7 +12,7 @@ public class RealignerTargetCreatorPerformanceTest extends WalkerTest {
         WalkerTestSpec spec1 = new WalkerTestSpec(
                 "-R " + hg18Reference +
                         " -T RealignerTargetCreator" +
-                        " -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod" +
+                        " -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
                         " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
                         " -L chr1:1-50,000,000" +
                         " -o /dev/null",
@@ -23,7 +23,7 @@ public class RealignerTargetCreatorPerformanceTest extends WalkerTest {
         WalkerTestSpec spec2 = new WalkerTestSpec(
                 "-R " + hg18Reference +
                         " -T RealignerTargetCreator" +
-                        " -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod" +
+                        " -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
                         " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" +
                         " -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" +
                         " -o /dev/null",