From 7ab8b5333930435a53716078956c6ff209633475 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Tue, 26 Jul 2011 11:37:31 -0400
Subject: [PATCH] Support for List<RodBinding> argument type

---
 .../sting/commandline/RodBinding.java             | 15 ++++++++++-----
 .../variantutils/VariantsToTableNewRodStyle.java  |  8 +++++++-
 2 files changed, 17 insertions(+), 6 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/commandline/RodBinding.java b/public/java/src/org/broadinstitute/sting/commandline/RodBinding.java
index 2f5046b3a..f4086fead 100644
--- a/public/java/src/org/broadinstitute/sting/commandline/RodBinding.java
+++ b/public/java/src/org/broadinstitute/sting/commandline/RodBinding.java
@@ -27,6 +27,7 @@ package org.broadinstitute.sting.commandline;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
 import java.util.List;
@@ -35,7 +36,7 @@ import java.util.List;
  *
  */
 // TODO -- should have a derived class called VariantContentRodBinding with simple accessors
-public class RodBinding<T> {
+public class RodBinding {
     final String variableName;
     final File sourceFile;
 
@@ -52,12 +53,16 @@ public class RodBinding<T> {
         return sourceFile;
     }
 
-    public List<T> getAll(RefMetaDataTracker tracker) {
-        return (List<T>)tracker.getReferenceMetaData(variableName);
+    public List<Object> getAll(RefMetaDataTracker tracker) {
+        return tracker.getReferenceMetaData(variableName);
     }
 
-    public T getVariantContext(RefMetaDataTracker tracker, ReferenceContext ref, GenomeLoc loc) {
-        return (T)tracker.getVariantContext(ref, variableName, loc);
+    public VariantContext getVariantContext(RefMetaDataTracker tracker, ReferenceContext ref, GenomeLoc loc) {
+        return tracker.getVariantContext(ref, variableName, loc);
+    }
+
+    public String toString() {
+        return String.format("(RodBinding name=%s source=%s)", variableName, sourceFile);
     }
 
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableNewRodStyle.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableNewRodStyle.java
index b44983e3d..552c5bd07 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableNewRodStyle.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableNewRodStyle.java
@@ -66,7 +66,10 @@ public class VariantsToTableNewRodStyle extends RodWalker<Integer, Integer> {
     public boolean ALLOW_MISSING_DATA = false;
 
     @Input(fullName="variants", shortName="V", doc="The variant file we will convert to a table", required=true)
-    public RodBinding<VariantContext> variants;
+    public RodBinding variants;
+
+    @Input(fullName="variantsList", shortName="VL", doc="The variant file we will convert to a table", required=true)
+    public List<RodBinding> variantsList;
 
     public void initialize() {
         out.println(Utils.join("\t", fieldsToTake));
@@ -135,6 +138,9 @@ public class VariantsToTableNewRodStyle extends RodWalker<Integer, Integer> {
         if ( tracker == null ) // RodWalkers can make funky map calls
             return 0;
 
+        for ( RodBinding binding : variantsList )
+            System.out.printf("VariantList binding %s%n", binding);
+
         if ( ++nRecords < MAX_RECORDS || MAX_RECORDS == -1 ) {
             VariantContext vc = variants.getVariantContext(tracker, ref, context.getLocation());
             if ( (keepMultiAllelic || vc.isBiallelic()) && ( showFiltered || vc.isNotFiltered() ) ) {