From a2a38a4bbb83b2ccf2acd29347e02558c3931681 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 10 Apr 2009 04:21:19 +0000
Subject: [PATCH] Removed RepairBadlyCombinedSamFile jar target.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@359 348d0f76-0448-11de-a6fe-93d51630548a
---
 build.xml | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/build.xml b/build.xml
index f715059f5..3386cafea 100644
--- a/build.xml
+++ b/build.xml
@@ -111,6 +111,17 @@
           </manifest>
         </jar>
 
+        <jar jarfile="dist/CombineSamAndFourProbs.jar" whenmanifestonly="skip">
+          <!--<fileset dir="build" includes="**/fourbasecaller/**/*.class" />-->
+          <fileset dir="build">
+            <include name="**/fourbasecaller/**/*.class" />
+            <include name="**/illumina/**/*.class" />
+          </fileset>
+          <manifest>
+            <attribute name="Main-Class" value="org.broadinstitute.sting.playground.fourbasecaller.CombineSamAndFourProbs" />
+          </manifest>
+        </jar>
+
         <jar jarfile="dist/Playground.jar" whenmanifestonly="skip">
             <fileset dir="build">
                 <include name="**/*.class"/>
@@ -143,6 +154,12 @@
             </manifest>
         </jar>
 
+        <jar jarfile="dist/CombineSamAndFourProbs.jar" update="true" whenmanifestonly="skip">
+            <manifest>
+                <attribute name="Class-Path" value="${jar.classpath}" />
+            </manifest>
+        </jar>
+
         <jar jarfile="dist/Playground.jar" update="true" whenmanifestonly="skip">
             <manifest>
                 <attribute name="Class-Path" value="${jar.classpath}"/>