From d83ad906eff14027908376eceb37dd502a6fdd78 Mon Sep 17 00:00:00 2001
From: Joel Thibault <thibault@broadinstitute.org>
Date: Mon, 26 Nov 2012 13:44:13 -0500
Subject: [PATCH] Add profile range contract

---
 .../sting/gatk/walkers/ActiveRegionWalker.java  |  2 ++
 .../traversals/TraverseActiveRegionsTest.java   | 17 +++++++++++++++++
 2 files changed, 19 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
index fed2c995e..c6e28df05 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers;
 
+import com.google.java.contract.Ensures;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broad.tribble.Feature;
 import org.broadinstitute.sting.commandline.Input;
@@ -75,6 +76,7 @@ public abstract class ActiveRegionWalker<MapType, ReduceType> extends Walker<Map
     }
 
     // Determine probability of active status over the AlignmentContext
+    @Ensures({"result.isActiveProb >= 0.0", "result.isActiveProb <= 1.0"})
     public abstract ActivityProfileResult isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context);
 
     // Map over the ActiveRegion
diff --git a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
index 018e92d84..8a4be48be 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.traversals;
 
+import com.google.java.contract.PreconditionError;
 import net.sf.samtools.*;
 import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.utils.interval.IntervalUtils;
@@ -52,6 +53,10 @@ public class TraverseActiveRegionsTest extends BaseTest {
             this.prob = 1.0;
         }
 
+        public DummyActiveRegionWalker(double constProb) {
+            this.prob = constProb;
+        }
+
         @Override
         public ActivityProfileResult isActive(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
             isActiveCalls.add(ref.getLocus());
@@ -132,6 +137,18 @@ public class TraverseActiveRegionsTest extends BaseTest {
         return activeIntervals;
     }
 
+    @Test (expectedExceptions = PreconditionError.class)
+    public void testIsActiveRangeLow () {
+        DummyActiveRegionWalker walker = new DummyActiveRegionWalker(-0.1);
+        getActiveRegions(walker, intervals).values();
+    }
+
+    @Test (expectedExceptions = PreconditionError.class)
+    public void testIsActiveRangeHigh () {
+        DummyActiveRegionWalker walker = new DummyActiveRegionWalker(1.1);
+        getActiveRegions(walker, intervals).values();
+    }
+
     @Test
     public void testActiveRegionCoverage() {
         DummyActiveRegionWalker walker = new DummyActiveRegionWalker();