From b8c0b05785e36015b3a839eac56cea00a9fd2b2e Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Fri, 25 Jan 2013 16:00:06 -0500
Subject: [PATCH] Add contract to ensure that getAdapterBoundary returns the
 right result

-- Also renamed the function to getAdaptorBoundary for consistency across the codebase
---
 .../src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java | 4 +++-
 .../src/org/broadinstitute/sting/utils/sam/ReadUtils.java     | 2 +-
 .../org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java | 2 +-
 3 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
index 62beb8814..504e718d0 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.utils.sam;
 
+import com.google.java.contract.Ensures;
 import net.sf.samtools.*;
 import org.broadinstitute.sting.utils.NGSPlatform;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@@ -579,7 +580,8 @@ public class GATKSAMRecord extends BAMRecord {
      *
      * @return the result of calling ReadUtils.getAdaptorBoundary on this read
      */
-    public int getAdapterBoundary() {
+    @Ensures("result == ReadUtils.getAdaptorBoundary(this)")
+    public int getAdaptorBoundary() {
         if ( adapterBoundary == null )
             adapterBoundary = ReadUtils.getAdaptorBoundary(this);
         return adapterBoundary;
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
index 3c0f9038b..c17e81b9c 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
@@ -169,7 +169,7 @@ public class ReadUtils {
      * @return whether or not the base is in the adaptor
      */
     public static boolean isBaseInsideAdaptor(final GATKSAMRecord read, long basePos) {
-        final int adaptorBoundary = read.getAdapterBoundary();
+        final int adaptorBoundary = read.getAdaptorBoundary();
         if (adaptorBoundary == CANNOT_COMPUTE_ADAPTOR_BOUNDARY || read.getInferredInsertSize() > DEFAULT_ADAPTOR_SIZE)
             return false;
 
diff --git a/public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java
index b11f2af24..7b48b1b69 100644
--- a/public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java
@@ -48,7 +48,7 @@ public class ReadUtilsUnitTest extends BaseTest {
         }});
 
         tests.add( new Object[]{ new GetAdaptorFunc() {
-            @Override public int getAdaptor(final GATKSAMRecord record) { return record.getAdapterBoundary(); }
+            @Override public int getAdaptor(final GATKSAMRecord record) { return record.getAdaptorBoundary(); }
         }});
 
         return tests.toArray(new Object[][]{});