From 9de06560df2fa46c5aba1642688b598568c4fc44 Mon Sep 17 00:00:00 2001
From: Menachem Fromer <fromer@broadinstitute.org>
Date: Thu, 11 Aug 2011 17:54:16 -0400
Subject: [PATCH] Update to new RodBinding system

---
 .../gatk/walkers/phasing/MergeMNPsWalker.java      | 12 +++++++-----
 .../MergeSegregatingAlternateAllelesWalker.java    | 14 ++++++--------
 .../walkers/phasing/MergeMNPsIntegrationTest.java  |  2 +-
 ...SegregatingAlternateAllelesIntegrationTest.java |  2 +-
 4 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java
index 14f54ec7d..809772c05 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java
@@ -25,11 +25,12 @@
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
@@ -58,7 +59,8 @@ public class MergeMNPsWalker extends RodWalker<Integer, Integer> {
     @Argument(fullName = "maxGenomicDistanceForMNP", shortName = "maxDistMNP", doc = "The maximum reference-genome distance between consecutive heterozygous sites to permit merging phased VCF records into a MNP record; [default:1]", required = false)
     protected int maxGenomicDistanceForMNP = 1;
 
-    private String rodName = "variant";
+    @Input(fullName="variant", shortName = "V", doc="Select variants from this VCF file", required=true)
+    public RodBinding<VariantContext> variants;
 
     public void initialize() {
         initializeVcfWriter();
@@ -74,8 +76,8 @@ public class MergeMNPsWalker extends RodWalker<Integer, Integer> {
         hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
         hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
 
-        Map<String, VCFHeader> rodNameToHeader = getVCFHeadersFromRods(getToolkit(), Arrays.asList(rodName));
-        vcMergerWriter.writeHeader(new VCFHeader(hInfo, new TreeSet<String>(rodNameToHeader.get(rodName).getGenotypeSamples())));
+        Map<String, VCFHeader> rodNameToHeader = getVCFHeadersFromRods(getToolkit(), Arrays.asList(variants.getName()));
+        vcMergerWriter.writeHeader(new VCFHeader(hInfo, new TreeSet<String>(rodNameToHeader.get(variants.getName()).getGenotypeSamples())));
     }
 
     public boolean generateExtendedEvents() {
@@ -98,7 +100,7 @@ public class MergeMNPsWalker extends RodWalker<Integer, Integer> {
         if (tracker == null)
             return null;
 
-        for (VariantContext vc : tracker.getValues(VariantContext.class, rodName, context.getLocation()))
+        for (VariantContext vc : tracker.getValues(variants, context.getLocation()))
             writeVCF(vc);
 
         return 0;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java
index e1be5e5c5..96d5c471f 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java
@@ -24,13 +24,10 @@
 
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Hidden;
-import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
@@ -81,7 +78,8 @@ public class MergeSegregatingAlternateAllelesWalker extends RodWalker<Integer, I
     @Argument(fullName = "dontRequireSomeSampleHasDoubleAltAllele", shortName = "dontRequireSomeSampleHasDoubleAltAllele", doc = "Should the requirement, that SUCCESSIVE records to be merged have at least one sample with a double alternate allele, be relaxed?; [default:false]", required = false)
     protected boolean dontRequireSomeSampleHasDoubleAltAllele = false;
 
-    private String rodName = "variant";
+    @Input(fullName="variant", shortName = "V", doc="Select variants from this VCF file", required=true)
+    public RodBinding<VariantContext> variants;
 
     public void initialize() {
         initializeVcfWriter();
@@ -111,8 +109,8 @@ public class MergeSegregatingAlternateAllelesWalker extends RodWalker<Integer, I
         hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
         hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
 
-        Map<String, VCFHeader> rodNameToHeader = getVCFHeadersFromRods(getToolkit(), Arrays.asList(rodName));
-        vcMergerWriter.writeHeader(new VCFHeader(hInfo, new TreeSet<String>(rodNameToHeader.get(rodName).getGenotypeSamples())));
+        Map<String, VCFHeader> rodNameToHeader = getVCFHeadersFromRods(getToolkit(), Arrays.asList(variants.getName()));
+        vcMergerWriter.writeHeader(new VCFHeader(hInfo, new TreeSet<String>(rodNameToHeader.get(variants.getName()).getGenotypeSamples())));
     }
 
     public boolean generateExtendedEvents() {
@@ -135,7 +133,7 @@ public class MergeSegregatingAlternateAllelesWalker extends RodWalker<Integer, I
         if (tracker == null)
             return null;
 
-        for (VariantContext vc : tracker.getValues(VariantContext.class, rodName, context.getLocation()))
+        for (VariantContext vc : tracker.getValues(variants, context.getLocation()))
             writeVCF(vc);
 
         return 0;
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsIntegrationTest.java
index c88eac149..2e4556af0 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsIntegrationTest.java
@@ -10,7 +10,7 @@ public class MergeMNPsIntegrationTest extends WalkerTest {
     public static String baseTestString(String reference, String VCF, int maxDistMNP) {
         return "-T MergeMNPs" +
                 " -R " + reference +
-                " -B:variant,VCF " + validationDataLocation + VCF +
+                " --variant:vcf " + validationDataLocation + VCF +
                 " --maxGenomicDistanceForMNP " + maxDistMNP +
                 " -o %s" +
                 " -NO_HEADER";
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesIntegrationTest.java
index f855c1dd3..db1e4a82f 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesIntegrationTest.java
@@ -10,7 +10,7 @@ public class MergeSegregatingAlternateAllelesIntegrationTest extends WalkerTest
     public static String baseTestString(String reference, String VCF, int maxDist) {
         return "-T MergeSegregatingAlternateAlleles" +
                 " -R " + reference +
-                " -B:variant,VCF " + validationDataLocation + VCF +
+                " --variant:vcf " + validationDataLocation + VCF +
                 " --maxGenomicDistance " + maxDist +
                 " -o %s" +
                 " -NO_HEADER";