From 85f2968104aade8802af021ed7f176a8d3eef660 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 29 Dec 2010 20:46:03 +0000
Subject: [PATCH] add convenience methods for RODs-for-reads: the ability to
 get all the RODs covering the read, regardless of their type or position on
 the read.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4912 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../providers/RODMetaDataContainer.java          | 15 ++++++++++++---
 .../sting/gatk/refdata/ReadMetaDataTracker.java  | 16 ++++++++++++----
 2 files changed, 24 insertions(+), 7 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/providers/RODMetaDataContainer.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/RODMetaDataContainer.java
index 36b02466d..180431ddd 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/RODMetaDataContainer.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/RODMetaDataContainer.java
@@ -40,14 +40,14 @@ import java.util.*;
  * stores both the name and the class for each ROD.  This class assumes that:
  *
  * -Names must be unique
- * -Classes are allowed to have dupplicates
+ * -Classes are allowed to have duplicates
  *
  * This class encapsulates the ref data associations, and provides lookup by name and by
  * class type.
  *
  */
 public class RODMetaDataContainer {
-    // we only allow non-dupplicate ROD names, a HashMap is fine
+    // we only allow non-duplicate ROD names, a HashMap is fine
     private final HashMap<String, GATKFeature> nameMap = new HashMap<String, GATKFeature>();
 
     // we do allow duplicate class entries, so we need to store pairs of data
@@ -59,11 +59,20 @@ public class RODMetaDataContainer {
     }
 
     public Collection<GATKFeature> getSet(String name) {
-        if (name == null) return nameMap.values();
+        if (name == null) return getSet();
         Set<GATKFeature> set = new HashSet<GATKFeature>();
         if (nameMap.containsKey(name)) set.add(nameMap.get(name));
         return set;
     }
+
+    /**
+     * get the feature contents of this container; the unfiltered set without their name association
+     * @return
+     */
+    public Collection<GATKFeature> getSet() {
+        return new ArrayList<GATKFeature>(nameMap.values());
+    }
+
     // the brute force (n) search ended up being faster than sorting and binary search in all but the most extreme cases (thousands of RODs at a location).
     public Collection<GATKFeature> getSet(Class cls) {
         Collection<GATKFeature> ret = new ArrayList<GATKFeature>();
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/ReadMetaDataTracker.java b/java/src/org/broadinstitute/sting/gatk/refdata/ReadMetaDataTracker.java
index 090022269..96dbd15f2 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/ReadMetaDataTracker.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/ReadMetaDataTracker.java
@@ -29,10 +29,7 @@ import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 
-import java.util.Collection;
-import java.util.LinkedHashMap;
-import java.util.Map;
-import java.util.TreeMap;
+import java.util.*;
 
 
 /**
@@ -168,4 +165,15 @@ public class ReadMetaDataTracker {
     public Map<Integer, Collection<GATKFeature>> getContigOffsetMapping(Class cl) {
         return createGenomeLocAlignment(record, mapping, cl, null);
     }
+
+    /**
+     * get the list of all the RODS overlapping this read, without any information about their position
+     * @return a Collection (no order guaranteed), of all the RODs covering this read
+     */
+    public List<GATKFeature> getAllCoveringRods() {
+        List<GATKFeature> ret = new ArrayList<GATKFeature>();
+        for (Map.Entry<Integer, RODMetaDataContainer> entry : mapping.entrySet())
+            ret.addAll(entry.getValue().getSet());
+        return ret;
+    }
 }