From 53db7b8faadb8987ef8d1e0056850208515b3821 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 8 Apr 2011 03:31:52 +0000
Subject: [PATCH] Did some refactoring which broke some unit tests, and then
 failed to run the unit tests.  Definitely not my best effort...

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5599 348d0f76-0448-11de-a6fe-93d51630548a
---
 java/test/net/sf/samtools/GATKBAMFileSpanUnitTest.java | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/java/test/net/sf/samtools/GATKBAMFileSpanUnitTest.java b/java/test/net/sf/samtools/GATKBAMFileSpanUnitTest.java
index b76306013..a9586c3c8 100644
--- a/java/test/net/sf/samtools/GATKBAMFileSpanUnitTest.java
+++ b/java/test/net/sf/samtools/GATKBAMFileSpanUnitTest.java
@@ -145,7 +145,7 @@ public class GATKBAMFileSpanUnitTest {
     public void testSubtractionOfEmptyChunkLists() {
         GATKBAMFileSpan regionOne = new GATKBAMFileSpan();
         GATKBAMFileSpan regionTwo = new GATKBAMFileSpan();
-        GATKBAMFileSpan subtraction = regionOne.subtract(regionTwo);
+        GATKBAMFileSpan subtraction = regionOne.minus(regionTwo);
         Assert.assertEquals(subtraction.getGATKChunks().size(),0,"Elements inserted in subtraction of two empty sets");
     }
 
@@ -153,7 +153,7 @@ public class GATKBAMFileSpanUnitTest {
     public void testSingleIntervalSubtractedAway() {
         GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,1<<16));
         GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(0,1<<16));
-        GATKBAMFileSpan subtraction = regionOne.subtract(regionTwo);
+        GATKBAMFileSpan subtraction = regionOne.minus(regionTwo);
         Assert.assertEquals(subtraction.getGATKChunks().size(),0,"Elements inserted in complete subtraction of region");
     }
 
@@ -161,7 +161,7 @@ public class GATKBAMFileSpanUnitTest {
     public void testMultipleIntervalsSubtractedAway() {
         GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk[] { new GATKChunk(0,1<<16), new GATKChunk(2<<16,3<<16) });
         GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk[] { new GATKChunk(0,1<<16), new GATKChunk(2<<16,3<<16) });
-        GATKBAMFileSpan subtraction = regionOne.subtract(regionTwo);
+        GATKBAMFileSpan subtraction = regionOne.minus(regionTwo);
         Assert.assertEquals(subtraction.getGATKChunks().size(),0,"Elements inserted in complete subtraction of region");
     }
 
@@ -169,7 +169,7 @@ public class GATKBAMFileSpanUnitTest {
     public void testSubtractionOfStrictSubset() {
         GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,2<<16));
         GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(0,1<<16));
-        GATKBAMFileSpan subtraction = regionOne.subtract(regionTwo);
+        GATKBAMFileSpan subtraction = regionOne.minus(regionTwo);
         Assert.assertEquals(subtraction.getGATKChunks().size(),1,"Incorrect size in strict subset subtraction of region");
         Assert.assertEquals(subtraction.getGATKChunks().get(0),new GATKChunk(1<<16,2<<16),"Determined subtraction is incorrect.");
     }
@@ -178,7 +178,7 @@ public class GATKBAMFileSpanUnitTest {
     public void testSubtractionOfPartialOverlap() {
         GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,2<<16));
         GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(1<<16,3<<16));
-        GATKBAMFileSpan subtraction = regionOne.subtract(regionTwo);
+        GATKBAMFileSpan subtraction = regionOne.minus(regionTwo);
         Assert.assertEquals(subtraction.getGATKChunks().size(),1,"Incorrect size in partial subset subtraction of region");
         Assert.assertEquals(subtraction.getGATKChunks().get(0),new GATKChunk(0<<16,1<<16),"Determined subtraction is incorrect.");
     }