From 7323b05dc1ed2e0cfdcd2d1b51480f63506d64b0 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sat, 19 Feb 2011 23:24:42 +0000
Subject: [PATCH] A simple utility for reordering a BAM file based on a new
 reference sequence.  This tool can be used to efficiently correct a
 lexicographically sorted BAM file

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5280 348d0f76-0448-11de-a6fe-93d51630548a
---
 build.xml | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/build.xml b/build.xml
index 881e741ed..a85e16e4a 100644
--- a/build.xml
+++ b/build.xml
@@ -358,6 +358,24 @@
           </manifest>
         </jar>
 
+        <jar jarfile="${dist.dir}/ReorderSam.jar" whenmanifestonly="skip">
+          <fileset dir="${java.classes}">
+            <include name="**/tools/**/*.class" />
+          </fileset>
+          <manifest>
+            <attribute name="Main-Class" value="org.broadinstitute.sting.playground.tools.ReorderSam" />
+          </manifest>
+        </jar>
+
+        <jar jarfile="${dist.dir}/CompareBAMAlignments.jar" whenmanifestonly="skip">
+          <fileset dir="${java.classes}">
+            <include name="**/tools/**/*.class" />
+          </fileset>
+          <manifest>
+            <attribute name="Main-Class" value="org.broadinstitute.sting.oneoffprojects.tools.CompareBAMAlignments" />
+          </manifest>
+        </jar>
+
         <subant target="dist" genericantfile="build.xml">
             <property name="build.dir" value="${external.build.dir}" />
             <property name="dist.dir" value="${external.dist.dir}" />
@@ -420,6 +438,18 @@
             </manifest>
         </jar>
 
+        <jar jarfile="${dist.dir}/CompareBAMAlignments.jar" update="true" whenmanifestonly="skip">
+            <manifest>
+                <attribute name="Class-Path" value="${jar.classpath}" />
+            </manifest>
+        </jar>
+
+        <jar jarfile="${dist.dir}/ReorderSam.jar" update="true" whenmanifestonly="skip">
+            <manifest>
+                <attribute name="Class-Path" value="${jar.classpath}" />
+            </manifest>
+        </jar>
+
     </target>
 
     <target name="queue.manifests" depends="queue.jar, init.manifests" if="scala.include">