[med-svn] [varscan] 01/02: add base build.xml fiel to build jar file, add patch to fix an upstream error in conversion

[Olivier Sallou]

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osallou pushed a commit to branch master
in repository varscan.

commit 9e4fe2b659e0a964665f4159d90f938dd8fb9798
Author: Olivier Sallou <olivier.sallou at irisa.fr>
Date:   Thu Apr 17 09:24:14 2014 +0200

    add base build.xml fiel to build jar file, add patch to fix an upstream error in conversion
---
 debian/build.xml           | 57 ++++++++++++++++++++++++++++++++++++++++++++++
 debian/patches/fix_convert | 20 ++++++++++++++++
 debian/patches/series      |  1 +
 3 files changed, 78 insertions(+)

diff --git a/debian/build.xml b/debian/build.xml
new file mode 100644
index 0000000..e62cd15
--- /dev/null
+++ b/debian/build.xml
@@ -0,0 +1,57 @@
+<?xml  version="1.0" ?>
+<project name="varscan" default="jar" basedir=".">
+    <!-- Directory structure -->
+    <property name="build.dir" location="build"/>
+    <property name="dist.dir" location="dist"/>
+    <property name="src.dir" location="net"/>
+    <property name="lib.dir" location="/usr/share/java"/>
+    <property name="class.dir" location="${build.dir}/classes"/>
+    
+    <property name="project.name" value="varscan"/>
+    <property name="debug" value="true"/>
+    <property name="optimized" value="true"/>
+    <property name="project.version" value="2.3.6"/>
+    <property environment="env"/>
+    <property name="project.jarfile.name" value="varscan.jar"/>   
+    
+    <property name="class.path" value=""/>
+                                
+    <path id="compile.classpath">
+            <fileset dir="${lib.dir}">
+            </fileset>
+            <fileset dir="${dist.dir}">
+                <include name="*.jar"/>
+            </fileset>
+    </path>
+    
+    
+    <target name="clean">
+        <echo level="info">Cleaning build directories</echo>
+        <delete verbose="true" includeEmptyDirs="true">
+            <fileset dir="${build.dir}" includes="**"/>
+            <fileset dir="${dist.dir}" includes="${project.name}*.jar"/>
+        </delete>
+    </target>
+    
+    <target name="compile">
+        <mkdir dir="${class.dir}"/>
+        <mkdir dir="${dist.dir}"/>
+        <javac srcdir="${src.dir}" destdir="${class.dir}" classpathref="compile.classpath" debug="${debug}" optimize="${optimized}" nowarn="true" source="1.6" target="1.6">
+        </javac>
+    </target>
+
+    <target name="jar" depends="compile">
+        <jar destfile="${dist.dir}/${project.jarfile.name}" basedir="${class.dir}" >
+         <manifest>
+             <attribute name="Built-By" value="Debian-Med team"/>
+             <attribute name="Main-Class" value="net.sf.varscan.VarScan"/>
+             <attribute name="Class-Path" value="${class.path}"/>
+             <attribute name="Specification-Title" value="varscan"/>
+             <attribute name="Specification-Version" value="${project.version}"/>
+          </manifest>
+        </jar>
+    </target>
+    
+</project>
+
+
diff --git a/debian/patches/fix_convert b/debian/patches/fix_convert
new file mode 100644
index 0000000..1e7cb82
--- /dev/null
+++ b/debian/patches/fix_convert
@@ -0,0 +1,20 @@
+Index: varscan/net/sf/varscan/CopyCaller.java
+===================================================================
+--- varscan.orig/net/sf/varscan/CopyCaller.java	2014-04-17 09:07:25.542896601 +0200
++++ varscan/net/sf/varscan/CopyCaller.java	2014-04-17 09:19:07.938907140 +0200
+@@ -253,7 +253,7 @@
+ 				    	        		int gcBin = (int) gcContent;
+ 				    	        		if(gcBin >= 0 && gcBin <= 100)
+ 				    	        		{
+-				    	        			gcLogSum[gcBin] += logratio;
++				    	        			gcLogSum[gcBin] += (float) logratio;
+ 				    	        			gcLogNum[gcBin]++;
+ 				    	        		}
+ 			    	        		}
+@@ -576,4 +576,4 @@
+ 		return(regionRef + "\t" + regionStart + "\t" + regionStop + "\t" + regionCalls + "\t" + regionDepthNormal + "\t" + regionDepthTumor + "\t" + log2ratio);
+ 
+ 	}
+-}
+\ No newline at end of file
++}
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..7dd2fe9
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+fix_convert

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