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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
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depristo 2011-02-19 23:24:42 +00:00
parent 444bf83acf
commit 7323b05dc1
1 changed files with 30 additions and 0 deletions
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30
build.xml
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@ -358,6 +358,24 @@
</manifest> </manifest>
</jar> </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"> <subant target="dist" genericantfile="build.xml">
<property name="build.dir" value="${external.build.dir}" /> <property name="build.dir" value="${external.build.dir}" />
<property name="dist.dir" value="${external.dist.dir}" /> <property name="dist.dir" value="${external.dist.dir}" />
@ -420,6 +438,18 @@
</manifest> </manifest>
</jar> </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>
<target name="queue.manifests" depends="queue.jar, init.manifests" if="scala.include"> <target name="queue.manifests" depends="queue.jar, init.manifests" if="scala.include">