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Added indel cleaner and quality scores recalibrator to the GATK package. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1311 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-07-24 16:20:38 +00:00
parent df44bdce7d
commit e2ec703a32
2 changed files with 14 additions and 0 deletions
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3
packages/CreatePackager.xsl
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@ -22,6 +22,9 @@
<jar jarfile="{concat($package.dir,$project.name,'.jar')}">
<classfileset dir="{$staging.dir}">
<root classname="{main-class}"/>
<xsl:for-each select="dependencies/package">
<rootfileset dir="{$staging.dir}" includes="{concat(translate(current(),'.','/'),'/','*.class')}" />
</xsl:for-each>
<xsl:for-each select="dependencies/class">
<root classname="{current()}" />
</xsl:for-each>

11
packages/GenomeAnalysisTK.xml
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@ -3,12 +3,23 @@
<name>GenomeAnalysisTK</name>
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<dependencies>
<package>org.broadinstitute.sting.gatk.filters</package>
<class>org.broadinstitute.sting.gatk.walkers.CountLociWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.CountReadsWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.DepthOfCoverageWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.PileupWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.PrintReadsWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.ValidatingPileupWalker</class>
<!-- Quality scores recalibration -->
<class>org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker</class>
<!-- Local realignment around indels -->
<class>org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.IntervalCleanerWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.IntervalMergerWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.MismatchIntervalWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.SNPClusterWalker</class>
</dependencies>
<resources>
<file>java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java</file>