From 7ce0df76f8819e43b791f677be7fba4e9bebe8ee Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 9 Nov 2009 04:25:39 +0000
Subject: [PATCH] Added accessors to the rod data sources so that walkers can
 access the name/file/type triplets for input rods.  This is necessary if e.g.
 you want to create a vcf writer based on all of the samples being input.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1994 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/GenomeAnalysisEngine.java             | 12 +++++++++++-
 .../ReferenceOrderedDataSource.java                  |  8 ++++++++
 .../sting/gatk/refdata/ReferenceOrderedData.java     |  6 +++++-
 3 files changed, 24 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 46030847a..1db9e406d 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -663,7 +663,7 @@ public class GenomeAnalysisEngine {
      * Returns data source object encapsulating all essential info and handlers used to traverse
      * reads; header merger, individual file readers etc can be accessed through the returned data source object.
      *
-     * @return
+     * @return the reads data source
      */
     public SAMDataSource getDataSource() {
         return this.readsDataSource;
@@ -677,4 +677,14 @@ public class GenomeAnalysisEngine {
     public GATKArgumentCollection getArguments() {
         return this.argCollection;
     }
+
+    /**
+     * Returns data source objects encapsulating all rod data;
+     * individual rods can be accessed through the returned data source objects.
+     *
+     * @return the rods data sources
+     */
+    public List<ReferenceOrderedDataSource> getRodDataSources() {
+        return this.rodDataSources;
+    }
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java
index e73458fbc..d24fdc61d 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java
@@ -53,6 +53,14 @@ public class ReferenceOrderedDataSource implements SimpleDataSource {
         return this.rod.getName();
     }
 
+    /**
+     * Return the underlying reference-ordered data.
+     * @return the underlying rod.
+     */
+    public ReferenceOrderedData getReferenceOrderedData() {
+        return this.rod;
+    }
+
     /**
      * Seek to the specified position and return an iterator through the data.
      * @param shard Shard that points to the selected position.
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java b/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
index b6edddabf..a878bd556 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
@@ -176,15 +176,19 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
     //
     // ----------------------------------------------------------------------
     public ReferenceOrderedData(final String name, File file, Class<ROD> type ) {
+        this.name = name;
         this.file = file;
         this.type = type;
-        this.name = name;
 //        this.header = initializeROD(name, file, type);
 //        this.fieldDelimiter = newROD(name, type).delimiterRegex();
     }
 
     public String getName() { return name; }
 
+    public File getFile() { return file; }
+
+    public Class<ROD> getType() { return type; }
+
     /**
      * Special equals override to see if this ROD is compatible with the given
      * name and type.  'Compatible' means that this ROD has the name that's passed