From c7f2d5c7c7d7a1c8ac46afebe321968d3bf78fd4 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Fri, 18 Nov 2011 14:49:06 -0500
Subject: [PATCH] Final minor fix to contract

---
 .../sting/utils/variantcontext/GenotypesContext.java       | 1 -
 .../sting/utils/variantcontext/VariantContextBuilder.java  | 7 ++++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java
index a639f512e..47e6b2fbe 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java
@@ -213,7 +213,6 @@ public class GenotypesContext implements List<Genotype> {
      * @param toCopy the collection of genotypes
      * @return an mutable GenotypeContext containing genotypes
      */
-    @Requires({"toCopy != null"})
     @Ensures({"result != null"})
     public static final GenotypesContext copy(final Collection<Genotype> toCopy) {
         return toCopy == null ? NO_GENOTYPES : create(new ArrayList<Genotype>(toCopy));
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java
index 67077e8c3..a2065d458 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java
@@ -24,7 +24,7 @@
 
 package org.broadinstitute.sting.utils.variantcontext;
 
-import com.google.java.contract.Requires;
+import com.google.java.contract.*;
 import org.broad.tribble.Feature;
 import org.broad.tribble.TribbleException;
 import org.broad.tribble.util.ParsingUtils;
@@ -158,10 +158,11 @@ public class VariantContextBuilder {
      * @return
      */
     @Requires({"key != null"})
+    @Ensures({"this.attributes.size() == old(this.attributes.size()) || this.attributes.size() == old(this.attributes.size()+1)"})
     public VariantContextBuilder attribute(final String key, final Object value) {
         if ( ! attributesCanBeModified ) {
             this.attributesCanBeModified = true;
-            this.attributes = new HashMap<String, Object>();
+            this.attributes = new HashMap<String, Object>(attributes);
         }
         attributes.put(key, value);
         return this;
@@ -282,7 +283,7 @@ public class VariantContextBuilder {
      * @param negLog10PError
      * @return
      */
-    @Requires("negLog10PError <= 0 || negLog10PError == VariantContext.NO_NEG_LOG_10PERROR")
+    @Requires("negLog10PError >= 0 || negLog10PError == VariantContext.NO_NEG_LOG_10PERROR")
     public VariantContextBuilder negLog10PError(final double negLog10PError) {
         this.negLog10PError = negLog10PError;
         return this;