Extract and include only the Tim Fennell-approved parts of picard private.

Hopefully this is a temporary solution and these classes will be migrated
into picard-public.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2041 348d0f76-0448-11de-a6fe-93d51630548a

build.xml

@@ -315,6 +315,32 @@
         <ant antfile="${dist}/packages/Build${executable}.xml" />
     </target>
 
+    <!-- Build a subset of picard with only those classes we need by completely abusing the packaging system -->
+    <!-- TODO: Reuse as much as possible of the 'stage' and 'package' targets -->
+    <target name="build-picard-private" depends="resolve">
+      <!-- Build out a classpath -->
+      <pathconvert property="required.picard.jars" pathsep=":">
+        <fileset dir="${basedir}">
+	  <include name="staging" />
+	  <include name="lib/picard-*.*.*.jar" />
+	  <include name="lib/sam-*.jar" />
+	</fileset>
+      </pathconvert>
+      <echo message="required.picard.jars=${required.picard.jars}" />
+
+      <!-- Stage picard-private -->
+      <delete dir="staging" />
+      <mkdir dir="staging" />
+      <unjar src="${picard.dist.dir}/picard-private.jar" dest="staging" overwrite="true" />
+
+      <!-- Use the packaging system to extract parts of picard-private we need -->
+      <mkdir dir="${dist}/packages" />
+      <xslt in="packages/PicardPrivate.xml" out="${dist}/packages/BuildPicardPrivate.xml" style="packages/CreatePackager.xsl" />
+      <ant antfile="${dist}/packages/BuildPicardPrivate.xml">
+	<property name="additional.jars" value="${required.picard.jars}" />
+      </ant>
+    </target>
+
     <target name="clean" description="clean up">
         <delete dir="out"/>
         <delete dir="build"/>

ivy.xml

@@ -8,7 +8,7 @@
   <dependencies defaultconf="default">
     <dependency org="net.sf" name="sam" rev="latest.integration" conf="default"/>
     <dependency org="net.sf" name="picard" rev="latest.integration" conf="default"/>
-    <dependency org="edu.mit.broad" name="picard-private" rev="latest.integration" conf="default"/>
+    <dependency org="edu.mit.broad" name="picard-private-parts" rev="latest.integration" conf="default"/>
     <dependency org="junit" name="junit" rev="4.4" conf="default"/>
     <dependency org="log4j" name="log4j" rev="1.2.15" conf="default"/>
     <dependency org="colt" name="colt" rev="1.2.0" conf="default"/>

packages/CreatePackager.xsl

@@ -3,6 +3,7 @@
 
   <xsl:variable name="ant.basedir" select="'${basedir}'" />
   <xsl:variable name="sting.dir" select="'${sting.dir}/'" />
+  <xsl:variable name="classpath" select="'${sting.dir}/staging:${additional.jars}'" />
   <xsl:variable name="dist.dir" select="'${sting.dir}/dist'" />
   <xsl:variable name="staging.dir" select="'${sting.dir}/staging'" />
   <xsl:variable name="package.dir" select="'${package.dir}/'" />
@@ -13,14 +14,14 @@
 
   <xsl:variable name="project.name" select="name" />
 
-  <project name="{$project.name}" default="package" basedir="..">
+  <project name="{$project.name}" default="package">
     <property name="sting.dir" value="{$ant.basedir}" />
     <property name="package.dir" value="{concat($dist.dir,'/packages/',$project.name)}" />
 
     <target name="package">
       <!-- Verify that all classes specified are present -->
       <xsl:for-each select="dependencies/class">
-	<available property="is.{current()}.present" classpath="{$staging.dir}" classname="{current()}"/>
+	<available property="is.{current()}.present" classpath="{$classpath}" classname="{current()}"/>
 	<fail message="Class {current()} not found" unless="is.{current()}.present" />
       </xsl:for-each>
 

packages/PicardPrivate.xml

@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<package>
+  <name>picard-private-parts</name>
+  <dependencies>
+    <class>edu.mit.broad.picard.directed.IntervalList</class>
+    <class>edu.mit.broad.picard.genotype.DiploidGenotype</class>
+    <class>edu.mit.broad.picard.genotype.geli.GeliFileReader</class>
+    <class>edu.mit.broad.picard.genotype.geli.GeliFileWriter</class>
+    <class>edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods</class>
+    <class>edu.mit.broad.picard.util.BasicTextFileParser</class>
+    <class>edu.mit.broad.picard.util.Interval</class>
+    <class>edu.mit.broad.picard.util.IntervalTree</class>
+    <class>edu.mit.broad.picard.util.OverlapDetector</class>
+    <class>edu.mit.broad.picard.util.PasteParser</class>
+  </dependencies>
+</package>

settings/repository/edu.mit.broad/picard-private-1109.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private" revision="1109" status="integration" publication="20091112172900" />
-</ivy-module>

settings/repository/edu.mit.broad/picard-private-parts-1109.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1109" status="integration" publication="20091112172900" />
+</ivy-module>