From b69c2d0f70dba9684a6cb4108f719d7c9778274a Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 26 Feb 2010 21:50:48 +0000
Subject: [PATCH] Cleanup.  Remove some unnecessary methods.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2900 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../shards/BAMFormatAwareShard.java           |  8 -------
 .../shards/BlockDelimitedReadShard.java       | 12 +++++------
 .../shards/IndexDelimitedLocusShard.java      | 21 -------------------
 3 files changed, 5 insertions(+), 36 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/BAMFormatAwareShard.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/BAMFormatAwareShard.java
index 5508d6db0..ca475b875 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/BAMFormatAwareShard.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/BAMFormatAwareShard.java
@@ -48,12 +48,4 @@ public interface BAMFormatAwareShard extends Shard {
      * @return An iterator over the reads stored in the shard.
      */
     public StingSAMIterator iterator();
-
-    /**
-     * Get the bounds of the current shard.  Current bounds
-     * will be the unfiltered extents of the current shard, from
-     * the start of the first interval to the end of the last interval.
-     * @return The bounds of the shard.
-     */
-    public GenomeLoc getBounds();
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShard.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShard.java
index e58551d2c..aea3a1d32 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShard.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShard.java
@@ -86,14 +86,12 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware
     }
 
     /**
-     * Get the bounds of the current shard.  Current bounds
-     * will be the unfiltered extents of the current shard, from
-     * the start of the first interval to the end of the last interval.
-     * @return The bounds of the shard.
+     * returns the type of shard.
      */
-    public GenomeLoc getBounds() {
-        return null;
-    }
+    @Override
+    public ShardType getShardType() {
+        return shardType;
+    }    
 
     /**
      * String representation of this shard.
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShard.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShard.java
index 7b89b7b98..3b01cd7ec 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShard.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShard.java
@@ -95,27 +95,6 @@ public class IndexDelimitedLocusShard extends LocusShard implements BAMFormatAwa
         return chunks;
     }
 
-    /**
-     * Get the bounds of the current shard.  Current bounds
-     * will be the unfiltered extents of the current shard, from
-     * the start of the first interval to the end of the last interval.
-     * @return The bounds of the shard.
-     */    
-    public GenomeLoc getBounds() {
-        if(loci == null)
-            return null;
-
-        String contig = null;
-        long start = Long.MAX_VALUE, stop = 0;
-        for(GenomeLoc locus: loci) {
-            if(contig == null) contig = locus.getContig();
-            start = Math.min(locus.getStart(),start);
-            stop = Math.max(locus.getStop(),stop);
-        }
-
-        return GenomeLocParser.createGenomeLoc(contig,start,stop);
-    }
-
     /**
      * returns the type of shard.
      */