From 4cfe0dd857891f6c70f4d0e58b60d6c4c401a0cd Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 7 Jul 2011 23:01:03 -0400
Subject: [PATCH 3/5] Test for bad alleles so that we don't generate
 IndexOutOfBoundsExceptions

---
 .../sting/utils/codecs/vcf/AbstractVCFCodec.java            | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
index cd0f52c68..01344a117 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
@@ -225,7 +225,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
             loc = pos + alleles.get(0).length() - 1;
         } else if ( !isSingleNucleotideEvent(alleles) ) {
             ArrayList<Allele> newAlleles = new ArrayList<Allele>();
-            loc = clipAlleles(pos, ref, alleles, newAlleles);
+            loc = clipAlleles(pos, ref, alleles, newAlleles, lineNo);
             alleles = newAlleles;
         }
 
@@ -504,7 +504,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
      * @param clippedAlleles output list of clipped alleles
      * @return a list of alleles, clipped to the reference
      */
-    protected static long clipAlleles(long position, String ref, List<Allele> unclippedAlleles, List<Allele> clippedAlleles) {
+    protected static long clipAlleles(long position, String ref, List<Allele> unclippedAlleles, List<Allele> clippedAlleles, int lineNo) {
 
         // Note that the computation of forward clipping here is meant only to see whether there is a common
         // base to all alleles, and to correctly compute reverse clipping,
@@ -522,6 +522,8 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
                 }
                 if (a.length() - reverseClipped <= forwardClipping || a.length() - forwardClipping == 0)
                     clipping = false;
+                else if (ref.length() == reverseClipped)
+                    generateException("bad alleles encountered", lineNo);
                 else if (a.getBases()[a.length()-reverseClipped-1] != ref.getBytes()[ref.length()-reverseClipped-1])
                     clipping = false;
             }

From a3c9d9c3ff561a0a910b5313e0ebb037b7883a4b Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Fri, 8 Jul 2011 15:34:39 -0400
Subject: [PATCH 5/5] Fixing Contracts for Java, and enabling contracts by
 default for unit/integration tests.

The NullPointerException we were seeing when trying to run with contracts enabled was being caused
by an outdated version of the asm library.

To run tests without contracts and disable their compilation, pass in "-Duse.contracts=false" to ant.

Also did some minor unrelated cleanup in build.xml
---
 build.xml                                     |  70 +++++++++++-------
 ivy.xml                                       |   4 +
 settings/ivysettings.xml                      |   1 +
 .../cofoja-1.0-20110609.jar                   | Bin
 .../cofoja-1.0-20110609.xml                   |   3 +
 5 files changed, 51 insertions(+), 27 deletions(-)
 rename settings/repository/{com.google => com.google.code.cofoja}/cofoja-1.0-20110609.jar (100%)
 create mode 100644 settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.xml

diff --git a/build.xml b/build.xml
index 2a23f74c1..986d89213 100644
--- a/build.xml
+++ b/build.xml
@@ -28,6 +28,7 @@
 
     <property name="build.dir" value="build" />
     <property name="dist.dir" value="dist" />
+    <property name="lib.dir" value="lib" />
     <property name="external.dir" value="external" />
     <property name="public.dir" value="public" />
     <property name="private.dir" value="private" />
@@ -44,11 +45,11 @@
     <property name="queue-extensions.source.dir" value="${build.dir}/queue-extensions/src" />
     
     <!-- Contracts for Java -->
-    <!-- uncomment out to enable building contracts -->
-    <property name="use.contracts" value="true" /> 
+    <!-- To disable, run with -Duse.contracts=false -->
+    <property name="use.contracts" value="true" />
     <property name="java.contracts" value="${build.dir}/java/contracts" />
-    <property name="cofojaDir" value="settings/repository/com.google/"/>
-    <property name="cofoja.jar" value="${cofojaDir}/cofoja-1.0-20110609.jar"/>
+    <property name="contracts.version" value="1.0-20110609" />
+    <property name="cofoja.jar" value="${lib.dir}/cofoja-${contracts.version}.jar"/>
     
     <!-- where to find the tribble distro -->
     <property name="tribble.dir" value="tribble" />
@@ -69,7 +70,7 @@
 
     <property environment="env"/>
 
-    <property name="drmaa.jar" value="${env.SGE_ROOT}/lib/drmaa.jar" />
+    <property name="drmaa.jar" value="${env.SGE_ROOT}/${lib.dir}/drmaa.jar" />
 
     <patternset id="java.source.pattern">
         <include name="${java.public.source.dir}/**/*.java" />
@@ -103,7 +104,7 @@
     </patternset>
     
     <path id="external.dependencies">
-      <fileset dir="lib">
+      <fileset dir="${lib.dir}">
         <patternset refid="dependency.mask" />
       </fileset>
     </path>
@@ -128,14 +129,14 @@
         <!-- ivy properties -->
         <property name="ivy.install.version" value="2.2.0"/>
         <property name="ivy.home" value="${user.home}/.ant"/>
-        <property name="ivy.jar.dir" value="${ivy.home}/lib"/>
+        <property name="ivy.jar.dir" value="${ivy.home}/${lib.dir}"/>
         <property name="ivy.jar.file" value="ivy-${ivy.install.version}.jar"/>
         <property name="ivy.settings.dir" value="settings"/>
         <property file="${ivy.settings.dir}/ivysettings.properties"/>
   
-      <mkdir dir="lib"/>
+      <mkdir dir="${lib.dir}"/>
       <mkdir dir="${ivy.jar.dir}"/>
-      <copy file="${cofoja.jar}" toFile="lib/cofoja.jar"/>
+
       <get src="http://repo1.maven.org/maven2/org/apache/ivy/ivy/${ivy.install.version}/${ivy.jar.file}"
            dest="${ivy.jar.dir}/${ivy.jar.file}"
            usetimestamp="true"/>
@@ -147,7 +148,7 @@
     </target>
 
     <target name="init.gridengine" depends="init" if="include.gridengine">
-        <copy todir="lib" file="${drmaa.jar}"/>
+        <copy todir="${lib.dir}" file="${drmaa.jar}"/>
     </target>
 
     <target name="resolve" depends="init.resolve,init,init.gridengine"
@@ -229,6 +230,10 @@
         <equals arg1="${gatk.target}" arg2="private" casesensitive="false" />
       </condition>
 
+      <condition property="include.contracts">
+        <equals arg1="${use.contracts}" arg2="true" />
+      </condition>
+
       <!-- Create the build directory structure used by compile -->
       <mkdir dir="${build.dir}"/>
       <mkdir dir="${java.classes}"/>
@@ -252,7 +257,7 @@
     <target name="init.scala.compile" depends="resolve"
             description="Initializes the scala ant tasks from scala-compiler.jar">
         <path id="scala.classpath">
-            <fileset dir="lib">
+            <fileset dir="${lib.dir}">
                 <include name="scala-compiler-*.jar"/>
                 <include name="scala-library-*.jar"/>
             </fileset>
@@ -287,7 +292,7 @@
             depends="gatk.compile.public.source,gatk.compile.private.source,gatk.compile.external.source" 
             description="compile the GATK source" />
 
-   <target name="gatk.contracts.public" depends="gatk.compile.source">
+   <target name="gatk.contracts.public" depends="gatk.compile.source" if="include.contracts">
         <javac fork="true" memoryMaximumSize="512m" srcdir="${java.public.source.dir}" destdir="${java.contracts}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" >
             <classpath>
                 <path refid="external.dependencies" />
@@ -299,7 +304,16 @@
         </javac>   
    </target>
 
-   <target name="gatk.contracts.private" depends="gatk.compile.source" if="include.private">
+    <target name="check.contracts.private" depends="gatk.contracts.public">
+        <condition property="include.contracts.private">
+          <and>
+            <isset property="include.contracts" />
+            <isset property="include.private" />
+          </and>
+        </condition>
+    </target>
+
+   <target name="gatk.contracts.private" depends="check.contracts.private" if="include.contracts.private">
         <javac fork="true" memoryMaximumSize="512m" srcdir="${java.private.source.dir}" destdir="${java.contracts}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" >
             <classpath>
                 <path refid="external.dependencies" />
@@ -312,7 +326,7 @@
    </target>
 
     <target name="gatk.contracts" depends="gatk.contracts.public,gatk.contracts.private" 
-            description="create GATK contracts" if="use.contracts" />
+            description="create GATK contracts" if="include.contracts" />
     
     <target name="gatk.compile" depends="tribble,init,resolve,gatk.compile.source,gatk.contracts" />
 
@@ -452,7 +466,7 @@
     <target name="init.jar" depends="sting.compile,extracthelp">
         <mkdir dir="${dist.dir}"/>
         <copy todir="${dist.dir}">
-            <fileset dir="lib" includes="*.jar"/>
+            <fileset dir="${lib.dir}" includes="*.jar"/>
         </copy>
     </target>
 
@@ -663,7 +677,7 @@
                 <path refid="external.dependencies" />
                 <pathelement location="${java.classes}"/>
                 <pathelement location="${java.contracts}"/>
-                <pathelement location="lib/testng-5.14.1.jar"/>
+                <pathelement location="${lib.dir}/testng-5.14.1.jar"/>
             </classpath>
             <compilerarg value="-proc:none"/>
 <!-- 
@@ -687,7 +701,7 @@
                 <path refid="scala.dependencies"/>
                 <pathelement location="${scala.test.classes}"/>
                 <pathelement location="${java.test.classes}"/>
-                <pathelement location="lib/testng-5.14.1.jar"/>
+                <pathelement location="${lib.dir}/testng-5.14.1.jar"/>
             </classpath>
         </scalac>
     </target>
@@ -727,9 +741,13 @@
                 <equals arg1="${pipeline.run}" arg2="$${pipeline.run}" />
             </condition>
 
+            <condition property="cofoja.jvm.args" value="-javaagent:${cofoja.jar} -Dcom.google.java.contract.log.contract=false" else="">
+                <isset property="include.contracts" />
+            </condition>
+
             <mkdir dir="${report}/@{testtype}"/>
             <echo message="Sting: Running @{testtype} test cases!"/>
-            <taskdef resource="testngtasks" classpath="lib/testng-5.14.1.jar"/>
+            <taskdef resource="testngtasks" classpath="${lib.dir}/testng-5.14.1.jar"/>
             <testng outputDir="${report}/@{testtype}"
                     haltOnFailure="false" failureProperty="test.failure"
                     verbose="2"
@@ -740,9 +758,7 @@
                 <jvmarg value="-Djava.awt.headless=true" />
                 <jvmarg value="-Dpipeline.run=${pipeline.run}" />
                 <jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
-                <!-- needs to be if -->
-                <!--jvmarg value="-javaagent:lib/cofoja.jar"/-->
-                <!--jvmarg value="-Dcom.google.java.contract.log.contract=false"/-->
+                <jvmarg line="${cofoja.jvm.args}"/>
 <!--                 <jvmarg value="-Xdebug"/> -->
 <!--                 <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> -->
                 <classpath>
@@ -820,7 +836,7 @@
 
     <!-- copy the compiled library -->
     <target name="tribble.compile.copy" description="Copies the compiled tribble library" depends="tribble.compile" if="tribble.compile.exists">
-        <copy todir="lib">
+        <copy todir="${lib.dir}">
             <fileset dir="${tribble.dir}/dist" includes="*.jar"/>
         </copy>
     </target>
@@ -828,7 +844,7 @@
     <!-- copy the precompiled library -->
     <target name="tribble.library.copy" description="Copies the precompiled tribble library" depends="tribble.init" unless="tribble.compile.exists">
         <echo message="Copying the Tribble Library..."/>
-        <copy todir="lib">
+        <copy todir="${lib.dir}">
             <fileset dir="settings/repository/org.broad" includes="tribble*.jar"/>
         </copy>
     </target>
@@ -921,8 +937,8 @@
       <pathconvert property="required.picard.jars" pathsep=":">
         <fileset dir="${basedir}">
 	     <include name="staging" />
-	     <include name="lib/picard-*.*.*.jar" />
-	     <include name="lib/sam-*.jar" />
+	     <include name="${lib.dir}/picard-*.*.*.jar" />
+	     <include name="${lib.dir}/sam-*.jar" />
 	   </fileset>
       </pathconvert>
       <echo message="required.picard.jars=${required.picard.jars}" />
@@ -944,7 +960,7 @@
     <!-- Find bug tasks                                                                   -->
     <!-- ******************************************************************************** -->
     <path id="findbugs.classpath">
-      <fileset dir="lib" erroronmissingdir="true" includes="*.jar"/>
+      <fileset dir="${lib.dir}" erroronmissingdir="true" includes="*.jar"/>
     </path>
     <target         name="findbugs" depends="dist">
         <antcall    target  ="resolve">
@@ -969,7 +985,7 @@
     <target name="clean" description="clean up" depends="tribble.clean,clean.javadoc">
         <delete dir="out"/>
         <delete dir="${build.dir}"/>
-        <delete dir="lib"/>
+        <delete dir="${lib.dir}"/>
         <delete dir="staging"/>
         <delete dir="${dist.dir}"/>
         <delete dir="pipelinetests"/>
diff --git a/ivy.xml b/ivy.xml
index c2a6c4ccd..ce724bc3c 100644
--- a/ivy.xml
+++ b/ivy.xml
@@ -60,6 +60,10 @@
     <dependency org="net.sourceforge.findbugs" name="jsr305" rev="1.3.2" conf="test"/>
     <dependency org="com.google.code.caliper" name="caliper" rev="1.0-SNAPSHOT" conf="test" />
 
+    <!-- Contracts for Java and dependencies -->
+    <dependency org="com.google.code.cofoja" name="cofoja" rev="1.0-20110609" />
+    <dependency org="asm" name="asm-all" rev="3.3.1" />
+
     <!-- POI, for reading pipeline files -->
     <dependency org="org.apache.poi" name="poi" rev="3.8-beta3" />
     <dependency org="org.apache.poi" name="poi-ooxml" rev="3.8-beta3" />
diff --git a/settings/ivysettings.xml b/settings/ivysettings.xml
index 1e47fa847..b77414df9 100644
--- a/settings/ivysettings.xml
+++ b/settings/ivysettings.xml
@@ -25,5 +25,6 @@
     <module organisation="javax.activation" resolver="java.net" />
     <module organisation="net.java.dev.jna" resolver="maven2-repository.dev.java.net" />
     <module organisation="com.google.code.caliper" resolver="projects" />
+    <module organisation="com.google.code.cofoja" resolver="projects" />
   </modules>
 </ivysettings>
diff --git a/settings/repository/com.google/cofoja-1.0-20110609.jar b/settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.jar
similarity index 100%
rename from settings/repository/com.google/cofoja-1.0-20110609.jar
rename to settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.jar
diff --git a/settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.xml b/settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.xml
new file mode 100644
index 000000000..38d4e88f1
--- /dev/null
+++ b/settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="com.google.code.cofoja" module="cofoja" revision="1.0-20110609" status="integration" publication="20110609114800" />
+</ivy-module>