From bc2d4f554d36fb858b48fff70a4af7ce674d1bda Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 9 Aug 2011 23:21:17 -0400
Subject: [PATCH] Bringing Indel Realigner up to speed with the new rod binding
 syntax; now use -known to specify the known indels track.

---
 .../sting/gatk/walkers/indels/IndelRealigner.java    | 12 ++++++------
 .../indels/IndelRealignerIntegrationTest.java        |  6 +++---
 .../indels/IndelRealignerPerformanceTest.java        |  4 ++--
 3 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index 61f21c488..cb7627888 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -30,10 +30,7 @@ import net.sf.samtools.*;
 import net.sf.samtools.util.RuntimeIOException;
 import net.sf.samtools.util.SequenceUtil;
 import net.sf.samtools.util.StringUtil;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Hidden;
-import org.broadinstitute.sting.commandline.Input;
-import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -86,6 +83,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
         USE_SW
     }
 
+    @Input(fullName="known", shortName = "known", doc="Input VCF file with known indels", required=false)
+    public RodBinding<VariantContext> known = RodBinding.makeUnbound(VariantContext.class);
+
     @Input(fullName="targetIntervals", shortName="targetIntervals", doc="intervals file output from RealignerTargetCreator", required=true)
     protected String intervalsFile = null;
 
@@ -558,8 +558,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                 if ( indelRodsSeen.contains(rod) )
                     continue;
                 indelRodsSeen.add(rod);
-                if ( VariantContextAdaptors.canBeConvertedToVariantContext(rod))
-                    knownIndelsToTry.add(VariantContextAdaptors.toVariantContext("", rod, ref));
+                if ( rod instanceof VariantContext )
+                    knownIndelsToTry.add((VariantContext)rod);
             }
         }
     }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
index 19dc99682..28e5a15de 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
@@ -28,7 +28,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
         executeTest("test realigner defaults", spec1);
 
         WalkerTestSpec spec2 = new WalkerTestSpec(
-                baseCommand + "-B:indels,vcf " + knownIndels,
+                baseCommand + "-known " + knownIndels,
                 1,
                 Arrays.asList(base_md5_with_SW_or_VCF));
         executeTest("test realigner defaults with VCF", spec2);
@@ -37,7 +37,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
     @Test
     public void testKnownsOnly() {
         WalkerTestSpec spec1 = new WalkerTestSpec(
-                baseCommand + "--consensusDeterminationModel KNOWNS_ONLY -B:indels,vcf " + knownIndels,
+                baseCommand + "--consensusDeterminationModel KNOWNS_ONLY -known " + knownIndels,
                 1,
                 Arrays.asList("3dd5d2c9931b375455af0bff1a2c4888"));
         executeTest("realigner known indels only from VCF", spec1);
@@ -46,7 +46,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
     @Test
     public void testUseSW() {
         WalkerTestSpec spec1 = new WalkerTestSpec(
-                baseCommand + "--consensusDeterminationModel USE_SW -B:indels,vcf " + knownIndels,
+                baseCommand + "--consensusDeterminationModel USE_SW -known " + knownIndels,
                 1,
                 Arrays.asList(base_md5_with_SW_or_VCF));
         executeTest("realigner use SW from VCF", spec1);
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
index 200b9b5a7..77675b0f4 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
@@ -30,7 +30,7 @@ public class IndelRealignerPerformanceTest extends WalkerTest {
                         " -LOD 5" +
                         " -maxConsensuses 100" +
                         " -greedy 100" +
-                        " -dbsnp:vcf " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
+                        " -known " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
                         " -o /dev/null" +
                         " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
                         " -L chr1:1-5,650,000" +
@@ -45,7 +45,7 @@ public class IndelRealignerPerformanceTest extends WalkerTest {
                         " -LOD 5" +
                         " -maxConsensuses 100" +
                         " -greedy 100" +
-                        " -dbsnp:vcf " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
+                        " -known " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
                         " -o /dev/null" +
                         " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" +
                         " -L chr1:1-150,000,000" +