From 224574424e90152ffbe4536a4dd6061eb886f9ff Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Fri, 8 Jul 2011 12:48:49 -0400
Subject: [PATCH 1/3] Bug fix: if we're genotyping a very long indel (>100 bp)
 fail gracefully instead of with an array out of bounds exception

---
 .../org/broadinstitute/sting/utils/genotype/Haplotype.java  | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java b/public/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java
index cb6557408..31791e805 100755
--- a/public/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java
+++ b/public/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java
@@ -133,8 +133,12 @@ public class Haplotype {
 
 
         byte[] basesBeforeVariant = Arrays.copyOfRange(refBases,startIdxInReference,startIdxInReference+numPrefBases);
+        int startAfter = startIdxInReference+numPrefBases+ refAllele.getBases().length;
+        // protect against long events that overrun available reference context
+        if (startAfter > refBases.length)
+            startAfter = refBases.length;
         byte[] basesAfterVariant = Arrays.copyOfRange(refBases,
-                startIdxInReference+numPrefBases+ refAllele.getBases().length, refBases.length);
+                startAfter, refBases.length);
 
 
         // Create location for all haplotypes

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 2/3] 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by an outdated version of the asm library.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>

From 8a78414432226daceccccb4b38463c0826fb0f19 Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Mon, 11 Jul 2011 12:10:11 -0400
Subject: [PATCH 3/3] Removed TileCovariate as a dependency for
 AnalyzeCovariates.jar

---
 public/packages/AnalyzeCovariates.xml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/public/packages/AnalyzeCovariates.xml b/public/packages/AnalyzeCovariates.xml
index 1862d6cbb..7e31934df 100644
--- a/public/packages/AnalyzeCovariates.xml
+++ b/public/packages/AnalyzeCovariates.xml
@@ -10,7 +10,6 @@
       <class name="org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate" />
       <class name="org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate" />
       <class name="org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate" />
-      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate" />
     </dependencies>
   </executable>
   <resources>