From 85ff983a591ee964dcf56cbe062a3573ec4f2c63 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 7 Mar 2011 23:00:17 +0000
Subject: [PATCH] Failed to include some required GenomeLoc utilities in my
 last commit.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5397 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/utils/GenomeLoc.java | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
index df0b358a5..a36248dfa 100644
--- a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
@@ -122,6 +122,17 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable, Serializable
                              Math.max( getStop(), that.getStop()) );
     }
 
+    /**
+     * Splits the contig into to regions: [start,split point) and [split point, end].
+     * @param splitPoint The point at which to split the contig.  Must be contained in the given interval.
+     * @return A two element array consisting of the genome loc before the split and the one after.
+     */
+    public GenomeLoc[] split(final int splitPoint) {
+        if(splitPoint < getStart() || splitPoint > getStop())
+            throw new ReviewedStingException(String.format("Unable to split contig %s at split point %d; split point is not contained in region.",this,splitPoint));
+        return new GenomeLoc[] { new GenomeLoc(getContig(),contigIndex,getStart(),splitPoint-1), new GenomeLoc(getContig(),contigIndex,splitPoint,getStop()) };
+    }
+
     public GenomeLoc intersect( GenomeLoc that ) throws ReviewedStingException {
         if(GenomeLoc.isUnmapped(this) || GenomeLoc.isUnmapped(that)) {
             if(! GenomeLoc.isUnmapped(this) || !GenomeLoc.isUnmapped(that))
@@ -171,6 +182,16 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable, Serializable
         return ( comparison == -1 || ( comparison == 0 && this.getStop() < that.getStart() ));        
     }
 
+    /**
+     * Tests whether any portion of this contig is before that contig.
+     * @param that Other contig to test.
+     * @return True if the start of this contig is before the start of the that contig.
+     */
+    public final boolean startsBefore(final GenomeLoc that) {
+        int comparison = this.compareContigs(that);
+        return ( comparison == -1 || ( comparison == 0 && this.getStart() < that.getStart() ));
+    }
+
     /**
      * Tests whether this contig is completely after contig 'that'.
      * @param that Contig to test against.