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Cleanup and formatting overhaul. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2652 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-01-21 19:22:56 +00:00
parent ee421c106c
commit 3e54e131e0
17 changed files with 218 additions and 250 deletions
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8
packages/Aligner.xml
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@ -1,11 +1,9 @@
<?xml version="1.0" encoding="UTF-8"?>
<package>
<name>Aligner</name>
<executable>
<name>Aligner</name>
<package name="Aligner">
<executable name="Aligner">
<dependencies>
<!-- BWA/C aligner implementation -->
<class>org.broadinstitute.sting.alignment.bwa.c.BWACAligner</class>
<class name="org.broadinstitute.sting.alignment.bwa.c.BWACAligner" />
</dependencies>
</executable>
</package>

22
packages/AnalyzeCovariates.xml
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@ -1,18 +1,16 @@
<?xml version="1.0" encoding="UTF-8"?>
<package>
<name>AnalyzeCovariates</name>
<executable>
<name>AnalyzeCovariates</name>
<main-class>org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates</main-class>
<properties>StingText.properties</properties>
<package name="AnalyzeCovariates">
<executable name="AnalyzeCovariates">
<main-class name="org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates" />
<resource-bundle file="StingText.properties" />
<dependencies>
<!-- Recalibration analysis script -->
<class>org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate</class>
<class name="org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates" />
<class name=">org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate" />
<class name=">org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate" />
<class name=">org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate" />
<class name=">org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate" />
<class name=">org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate" />
</dependencies>
</executable>
</package>

38
packages/CreatePackager.xsl
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@ -12,7 +12,7 @@
<xsl:template match="package">
<xsl:output method="xml" indent="yes"/>
<xsl:variable name="project.name" select="name" />
<xsl:variable name="project.name" select="@name" />
<project name="{$project.name}" default="package">
<property name="sting.dir" value="{$ant.basedir}" />
@ -21,12 +21,12 @@
<target name="package">
<!-- Verify that all classes specified are present -->
<xsl:for-each select="//class">
<available property="is.{current()}.present" classpath="{$classpath}" classname="{current()}"/>
<fail message="Class {current()} not found" unless="is.{current()}.present" />
<available property="is.{@name}.present" classpath="{$classpath}" classname="{@name}"/>
<fail message="Class {@name} not found" unless="is.{@name}.present" />
</xsl:for-each>
<xsl:for-each select="//resource-bundle">
<available property="is.{current()}.present" file="{$staging.dir}/{current()}"/>
<fail message="Resource bundle {current()} not found" unless="is.{current()}.present" />
<available property="is.{@file}.present" file="{$staging.dir}/{@file}"/>
<fail message="Resource bundle {@file} not found" unless="is.{@file}.present" />
</xsl:for-each>
<!-- Create an output directory for the package -->
@ -37,13 +37,13 @@
<!-- Add in other modules -->
<xsl:for-each select="modules/module">
<xsl:apply-templates select="document(current())/package/executable" />
<xsl:apply-templates select="document(@file)/package/executable" />
</xsl:for-each>
<!-- Include various script files -->
<xsl:for-each select="scripts/file">
<xsl:call-template name="symlink">
<xsl:with-param name="file.name" select="." />
<xsl:with-param name="file.name" select="@name" />
<xsl:with-param name="target.dir" select="$package.dir" />
</xsl:call-template>
</xsl:for-each>
@ -52,7 +52,7 @@
<xsl:for-each select="resources/file">
<mkdir dir="{$resources.dir}"/>
<xsl:call-template name="symlink">
<xsl:with-param name="file.name" select="." />
<xsl:with-param name="file.name" select="@name" />
<xsl:with-param name="target.dir" select="$resources.dir" />
</xsl:call-template>
</xsl:for-each>
@ -62,14 +62,14 @@
<xsl:when test="version">
<property file="{$staging.dir}/{version/@file}" />
<xsl:variable name="version.property" select="concat('${',version/@property,'}')" />
<property name="package.filename" value="{name}-{$version.property}.tar.bz2" />
<property name="package.filename" value="{@name}-{$version.property}.tar.bz2" />
</xsl:when>
<xsl:otherwise>
<property name="package.filename" value="{name}.tar.bz2" />
<property name="package.filename" value="{@name}.tar.bz2" />
</xsl:otherwise>
</xsl:choose>
<xsl:variable name="package.filename" select="'${package.filename}'" />
<tar destfile="{$dist.dir}/{$package.filename}" basedir="{$package.dir}" compression="bzip2" />
<tar destfile="{$dist.dir}/packages/{$package.filename}" basedir="{$package.dir}" compression="bzip2" />
</target>
</project>
</xsl:template>
@ -98,19 +98,19 @@
<!-- Transform an executable tag into an ant 'jar' task with nested fileset -->
<xsl:template match="executable">
<!-- Create a jar file containing the specified classes / packages and all their dependencies -->
<jar jarfile="{$package.dir}/{name}.jar">
<jar jarfile="{$package.dir}/{@name}.jar">
<classfileset dir="{$staging.dir}">
<root classname="{main-class}"/>
<root classname="{main-class/@name}"/>
</classfileset>
<xsl:for-each select="resource-bundle">
<fileset file="{$staging.dir}/{current()}" />
<fileset file="{$staging.dir}/{@file}" />
</xsl:for-each>
<xsl:for-each select="modules/module">
<xsl:apply-templates select="document(current())/package/executable/dependencies" />
<xsl:apply-templates select="document(@file)/package/executable/dependencies" />
</xsl:for-each>
<xsl:apply-templates select="dependencies" />
<manifest>
<attribute name="Main-Class" value="{main-class}"/>
<attribute name="Main-Class" value="{main-class/@name}"/>
</manifest>
</jar>
</xsl:template>
@ -119,14 +119,14 @@
<xsl:template match="dependencies">
<classfileset dir="{$staging.dir}">
<xsl:for-each select="package">
<rootfileset dir="{$staging.dir}" includes="{concat(translate(current(),'.','/'),'/','*.class')}" />
<rootfileset dir="{$staging.dir}" includes="{concat(translate(@name,'.','/'),'/','*.class')}" />
</xsl:for-each>
<xsl:for-each select="class">
<root classname="{current()}" />
<root classname="{@name}" />
</xsl:for-each>
</classfileset>
<xsl:for-each select="file">
<fileset file="{$staging.dir}/{current()}" />
<fileset file="{$staging.dir}/{@name}" />
</xsl:for-each>
</xsl:template>

12
packages/FindContaminatingReadGroups.xml
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@ -1,12 +1,10 @@
<?xml version="1.0" encoding="UTF-8"?>
<package>
<name>FindContaminatingReadGroups</name>
<executable>
<name>FindContaminatingReadGroups</name>
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<properties>StingText.properties</properties>
<package name="FindContaminatingReadGroups">
<executable name="FindContaminatingReadGroups">
<main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
<resource-bundle file="StingText.properties" />
<dependencies>
<class>org.broadinstitute.sting.playground.gatk.walkers.contamination.FindContaminatingReadGroupsWalker</class>
<class name="org.broadinstitute.sting.playground.gatk.walkers.contamination.FindContaminatingReadGroupsWalker" />
</dependencies>
</executable>
</package>

13
packages/FixBAMSortOrder.xml
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@ -1,14 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
<package>
<name>FixBAMSortOrder</name>
<executable>
<name>GenomeAnalysisTK</name>
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<package name="FixBAMSortOrder">
<executable name="FixBAMSortOrder">
<main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
<resource-bundle file="StingText.properties" />
<dependencies>
<!-- Text extracted from the javadocs -->
<properties>StingText.properties</properties>
<!-- The walker -->
<class>org.broadinstitute.sting.gatk.walkers.FixBAMSortOrderTag</class>
<class name="org.broadinstitute.sting.gatk.walkers.FixBAMSortOrderTag" />
</dependencies>
</executable>
</package>

26
packages/GATK-GSA-Pipeline.xml
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@ -1,25 +1,23 @@
<?xml version="1.0" encoding="UTF-8"?>
<!-- NOTE: Uses playground.
ant clean playground package -Dexecutable=GATK-GSA-Pipeline -->
<package>
<name>GATK-GSA-Pipeline</name>
<package name="GATK-GSA-Pipeline">
<version file="StingText.properties" property="org.broadinstitute.sting.gatk.version" />
<executable>
<name>GATK-GSA-Pipeline</name>
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<resource-bundle>StingText.properties</resource-bundle>
<executable name="GATK-GSA-Pipeline">
<main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
<resource-bundle file="StingText.properties" />
<modules>
<module>QualityScoresRecalibration.xml</module>
<module>LocalRealignmentAroundIndels.xml</module>
<module>UnifiedGenotyper.xml</module>
<module>VariantFiltration.xml</module>
<module>VariantAnnotator.xml</module>
<module>VariantEval.xml</module>
<module>FindContaminatingReadGroups.xml</module>
<module name="QualityScoresRecalibration.xml" />
<module name="LocalRealignmentAroundIndels.xml" />
<module name="UnifiedGenotyper.xml" />
<module name="VariantFiltration.xml" />
<module name="VariantAnnotator.xml" />
<module name="VariantEval.xml" />
<module name="FindContaminatingReadGroups.xml" />
</modules>
<dependencies>
<!-- Filters -->
<package>org.broadinstitute.sting.gatk.filters</package>
<package name="org.broadinstitute.sting.gatk.filters" />
</dependencies>
</executable>
</package>

74
packages/GATK-Picard.xml
View File

@ -2,55 +2,53 @@
<!-- In order to update this file, copy GenomeAnalysisTK.xml, change the name of the
package and executable to GATK-Picard, and add TileCovariate to the list of dependencies.
Remove the AnalyzeCovariates executable. -->
<package>
<name>GATK-Picard</name>
<package name="GATK-Picard">
<version file="StingText.properties" property="org.broadinstitute.sting.gatk.version" />
<executable>
<name>GATK-Picard</name>
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<resource-bundle>StingText.properties</resource-bundle>
<executable name="GATK-Picard">
<main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
<resource-bundle file="StingText.properties" />
<modules>
<module>QualityScoresRecalibration.xml</module>
<module>LocalRealignmentAroundIndels.xml</module>
<module>UnifiedGenotyper.xml</module>
<module>VariantFiltration.xml</module>
<module>VariantAnnotator.xml</module>
<module name="QualityScoresRecalibration.xml" />
<module name="LocalRealignmentAroundIndels.xml" />
<module name="UnifiedGenotyper.xml" />
<module name="VariantFiltration.xml" />
<module name="VariantAnnotator.xml" />
</modules>
<dependencies>
<!-- Filters -->
<package>org.broadinstitute.sting.gatk.filters</package>
<class>org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.PileupWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.PrintReadsWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker</class>
<package name="org.broadinstitute.sting.gatk.filters" />
<class name="org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker" />
<class name="org.broadinstitute.sting.gatk.walkers.PileupWalker" />
<class name="org.broadinstitute.sting.gatk.walkers.PrintReadsWalker" />
<class name="org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker" />
<class name="org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker" />
<class name="org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker" />
<!-- Recalibration Covariates -->
<class>org.broadinstitute.sting.gatk.walkers.recalibration.PositionCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.MinimumNQSCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.MappingQualityCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.PrimerRoundCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.HomopolymerCovariate</class>
<class name="org.broadinstitute.sting.gatk.walkers.recalibration.PositionCovariate" />
<class name="org.broadinstitute.sting.gatk.walkers.recalibration.MinimumNQSCovariate" />
<class name="org.broadinstitute.sting.gatk.walkers.recalibration.MappingQualityCovariate" />
<class name="org.broadinstitute.sting.gatk.walkers.recalibration.PrimerRoundCovariate" />
<class name="org.broadinstitute.sting.gatk.walkers.recalibration.HomopolymerCovariate" />
</dependencies>
</executable>
<resources>
<!-- GATK sample code and build scripts -->
<file>java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/examples/build.xml</file>
<file name="java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java" />
<file name="java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java" />
<file name="java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java" />
<file name="java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java" />
<file name="java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java" />
<file name="java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java" />
<file name="java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java" />
<file name="java/src/org/broadinstitute/sting/gatk/examples/build.xml" />
<!-- Sample reads and reference files -->
<file>testdata/exampleBAM.bam</file>
<file>testdata/exampleBAM.bam.bai</file>
<file>testdata/exampleFASTA.fasta</file>
<file>testdata/exampleFASTA.fasta.fai</file>
<file>testdata/exampleFASTA.dict</file>
<file name="testdata/exampleBAM.bam" />
<file name="testdata/exampleBAM.bam.bai" />
<file name="testdata/exampleFASTA.fasta" />
<file name="testdata/exampleFASTA.fasta.fai" />
<file name="testdata/exampleFASTA.dict" />
<!-- Supplemental scripts for graph generation, etc. -->
<file>R/plot_residualError_OtherCovariate.R</file>
<file>R/plot_residualError_QualityScoreCovariate.R</file>
<file name="R/plot_residualError_OtherCovariate.R" />
<file name="R/plot_residualError_QualityScoreCovariate.R" />
</resources>
</package>

31
packages/GATKResources.xml
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@ -1,20 +1,19 @@
<?xml version="1.0" encoding="UTF-8"?>
<package>
<name>GATKResources</name>
<package name="GATKResources">
<resources>
<file>/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod</file>
<file>/humgen/gsa-scr1/GATK_Data/dbsnp_130_b36.rod</file>
<file>/broad/1KG/reference/human_b36_both.fasta</file>
<file>/broad/1KG/reference/human_b36_both.dict</file>
<file>/broad/1KG/reference/human_b36_both.fasta.fai</file>
<file>/humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod</file>
<file>/humgen/gsa-scr1/GATK_Data/dbsnp_130_hg18.rod</file>
<file>/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta</file>
<file>/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.dict</file>
<file>/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta.fai</file>
<file>/humgen/gsa-scr1/GATK_Data/dbsnp_130_b37.rod</file>
<file>/broad/1KG/reference/human_g1k_v37.fasta</file>
<file>/broad/1KG/reference/human_g1k_v37.dict</file>
<file>/broad/1KG/reference/human_g1k_v37.fasta.fai</file>
<file name="/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" />
<file name="/humgen/gsa-scr1/GATK_Data/dbsnp_130_b36.rod" />
<file name="/broad/1KG/reference/human_b36_both.fasta" />
<file name="/broad/1KG/reference/human_b36_both.dict" />
<file name="/broad/1KG/reference/human_b36_both.fasta.fai" />
<file name="/humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod" />
<file name="/humgen/gsa-scr1/GATK_Data/dbsnp_130_hg18.rod" />
<file name="/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" />
<file name="/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.dict" />
<file name="/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta.fai" />
<file name="/humgen/gsa-scr1/GATK_Data/dbsnp_130_b37.rod" />
<file name="/broad/1KG/reference/human_g1k_v37.fasta" />
<file name="/broad/1KG/reference/human_g1k_v37.dict" />
<file name="/broad/1KG/reference/human_g1k_v37.fasta.fai" />
</resources>
</package>

68
packages/GenomeAnalysisTK.xml
View File

@ -1,52 +1,50 @@
<?xml version="1.0" encoding="UTF-8"?>
<package>
<name>GenomeAnalysisTK</name>
<package name="GenomeAnalysisTK">
<version file="StingText.properties" property="org.broadinstitute.sting.gatk.version" />
<executable>
<name>GenomeAnalysisTK</name>
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<resource-bundle>StingText.properties</resource-bundle>
<executable name="GenomeAnalysisTK">
<main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
<resource-bundle file="StingText.properties" />
<modules>
<module>QualityScoresRecalibration.xml</module>
<module>LocalRealignmentAroundIndels.xml</module>
<module>UnifiedGenotyper.xml</module>
<module>VariantFiltration.xml</module>
<module>VariantAnnotator.xml</module>
<module>VCFValidator.xml</module>
<module file="QualityScoresRecalibration.xml" />
<module file="LocalRealignmentAroundIndels.xml" />
<module file="UnifiedGenotyper.xml" />
<module file="VariantFiltration.xml" />
<module file="VariantAnnotator.xml" />
<module file="VCFValidator.xml" />
</modules>
<dependencies>
<!-- Filters -->
<package>org.broadinstitute.sting.gatk.filters</package>
<package name="org.broadinstitute.sting.gatk.filters" />
<!-- Basic qc walkers -->
<class>org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.PileupWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.PrintReadsWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker</class>
<class name="org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker" />
<class name="org.broadinstitute.sting.gatk.walkers.PileupWalker" />
<class name="org.broadinstitute.sting.gatk.walkers.PrintReadsWalker" />
<class name="org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker" />
<class name="org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker" />
<class name="org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker" />
</dependencies>
</executable>
<modules>
<module>AnalyzeCovariates.xml</module>
<module file="AnalyzeCovariates.xml"/>
</modules>
<resources>
<!-- GATK sample code and build scripts -->
<file>java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/examples/build.xml</file>
<file name="java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java" />
<file name="java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java" />
<file name="java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java" />
<file name="java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java" />
<file name="java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java" />
<file name="java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java" />
<file name="java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java" />
<file name="java/src/org/broadinstitute/sting/gatk/examples/build.xml" />
<!-- Sample reads and reference files -->
<file>testdata/exampleBAM.bam</file>
<file>testdata/exampleBAM.bam.bai</file>
<file>testdata/exampleFASTA.fasta</file>
<file>testdata/exampleFASTA.fasta.fai</file>
<file>testdata/exampleFASTA.dict</file>
<file name="testdata/exampleBAM.bam" />
<file name="testdata/exampleBAM.bam.bai" />
<file name="testdata/exampleFASTA.fasta" />
<file name="testdata/exampleFASTA.fasta.fai" />
<file name="testdata/exampleFASTA.dict" />
<!-- Supplemental scripts for graph generation, etc. -->
<file>R/plot_residualError_OtherCovariate.R</file>
<file>R/plot_residualError_QualityScoreCovariate.R</file>
<file name="R/plot_residualError_OtherCovariate.R" />
<file name="R/plot_residualError_QualityScoreCovariate.R" />
</resources>
</package>

26
packages/LocalRealignmentAroundIndels.xml
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@ -1,20 +1,18 @@
<?xml version="1.0" encoding="UTF-8"?>
<package>
<name>LocalRealignmentAroundIndels</name>
<executable>
<name>LocalRealignmentAroundIndels</name>
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<properties>StingText.properties</properties>
<package name="LocalRealignmentAroundIndels">
<executable name="LocalRealignmentAroundIndels">
<main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
<resource-bundle file="StingText.properties" />
<dependencies>
<!-- 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>
<class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperV2Walker</class>
<class name="org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector" />
<class name="org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker" />
<class name="org.broadinstitute.sting.gatk.walkers.indels.IntervalCleanerWalker" />
<class name="org.broadinstitute.sting.gatk.walkers.indels.IntervalMergerWalker" />
<class name="org.broadinstitute.sting.gatk.walkers.indels.MismatchIntervalWalker" />
<class name="org.broadinstitute.sting.gatk.walkers.indels.SNPClusterWalker" />
<class name="org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperWalker" />
<class name="org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperV2Walker" />
</dependencies>
</executable>
</package>

52
packages/PicardPrivate.xml
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@ -1,32 +1,30 @@
<?xml version="1.0" encoding="UTF-8"?>
<package>
<name>picard-private-parts</name>
<executable>
<name>picard-private-parts</name>
<package name="picard-private-parts">
<executable name="picard-private-parts">
<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.illumina.parser.IlluminaUtil</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>
<class>edu.mit.broad.picard.variation.KnownVariantCodecV2</class>
<class>edu.mit.broad.picard.variation.KnownVariantCodec</class>
<class>edu.mit.broad.picard.variation.KnownVariantFileHeader</class>
<class>edu.mit.broad.picard.variation.GenerateDbSnpFile</class>
<class>edu.mit.broad.picard.variation.VariantType</class>
<class>edu.mit.broad.picard.variation.ObsoleteKnownVariantCodecV1</class>
<class>edu.mit.broad.picard.variation.AbstractKnownVariantCodec</class>
<class>edu.mit.broad.picard.variation.KnownVariantIterator</class>
<class>edu.mit.broad.picard.variation.KnownVariantCodecFactory</class>
<class>edu.mit.broad.picard.variation.KnownVariant</class>
<class>edu.mit.broad.picard.variation.DbSnpFileReader</class>
<class>edu.mit.broad.picard.variation.DbSnpFileGenerator</class>
<class name="edu.mit.broad.picard.directed.IntervalList" />
<class name="edu.mit.broad.picard.genotype.DiploidGenotype" />
<class name="edu.mit.broad.picard.genotype.geli.GeliFileReader" />
<class name="edu.mit.broad.picard.genotype.geli.GeliFileWriter" />
<class name="edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods" />
<class name="edu.mit.broad.picard.util.BasicTextFileParser" />
<class name="edu.mit.broad.picard.illumina.parser.IlluminaUtil" />
<class name="edu.mit.broad.picard.util.Interval" />
<class name="edu.mit.broad.picard.util.IntervalTree" />
<class name="edu.mit.broad.picard.util.OverlapDetector" />
<class name="edu.mit.broad.picard.util.PasteParser" />
<class name="edu.mit.broad.picard.variation.KnownVariantCodecV2" />
<class name="edu.mit.broad.picard.variation.KnownVariantCodec" />
<class name="edu.mit.broad.picard.variation.KnownVariantFileHeader" />
<class name="edu.mit.broad.picard.variation.GenerateDbSnpFile" />
<class name="edu.mit.broad.picard.variation.VariantType" />
<class name="edu.mit.broad.picard.variation.ObsoleteKnownVariantCodecV1" />
<class name="edu.mit.broad.picard.variation.AbstractKnownVariantCodec" />
<class name="edu.mit.broad.picard.variation.KnownVariantIterator" />
<class name="edu.mit.broad.picard.variation.KnownVariantCodecFactory" />
<class name="edu.mit.broad.picard.variation.KnownVariant" />
<class name="edu.mit.broad.picard.variation.DbSnpFileReader" />
<class name="edu.mit.broad.picard.variation.DbSnpFileGenerator" />
</dependencies>
</executable>
</package>

24
packages/QualityScoresRecalibration.xml
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@ -1,20 +1,18 @@
<?xml version="1.0" encoding="UTF-8"?>
<package>
<name>QualityScoresRecalibration</name>
<executable>
<name>QualityScoresRecalibration</name>
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<properties>StingText.properties</properties>
<package name="QualityScoresRecalibration">
<executable name="QualityScoresRecalibration">
<main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
<resource-bundle file="StingText.properties" />
<dependencies>
<!-- Quality scores recalibration -->
<class>org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker</class>
<class file="org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker" />
<class file=">org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker" />
<!-- Recalibration Covariates -->
<class>org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate</class>
<class file=">org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate" />
<class file=">org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate" />
<class file=">org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate" />
<class file=">org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate" />
<class file=">org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate" />
</dependencies>
</executable>
</package>

12
packages/UnifiedGenotyper.xml
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@ -1,13 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
<package>
<name>UnifiedGenotyper</name>
<executable>
<name>UnifiedGenotyper</name>
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<properties>StingText.properties</properties>
<package name="UnifiedGenotyper">
<executable name="UnifiedGenotyper">
<main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
<resource-bundle file="StingText.properties" />
<dependencies>
<!-- Unified genotyper -->
<class>org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper</class>
<class name="org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper" />
</dependencies>
</executable>
</package>

12
packages/VCFValidator.xml
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@ -1,13 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
<package>
<name>VCFValidator</name>
<executable>
<name>VCFValidator</name>
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<properties>StingText.properties</properties>
<package name="VCFValidator">
<executable name="VCFValidator">
<main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
<resource-bundle file="StingText.properties" />
<dependencies>
<!-- VCF validator -->
<class>org.broadinstitute.sting.gatk.walkers.qc.VCFValidator</class>
<class name="org.broadinstitute.sting.gatk.walkers.qc.VCFValidator" />
</dependencies>
</executable>
</package>

26
packages/VariantAnnotator.xml
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@ -1,21 +1,19 @@
<?xml version="1.0" encoding="UTF-8"?>
<package>
<name>VariantAnnotator</name>
<executable>
<name>VariantAnnotator</name>
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<properties>StingText.properties</properties>
<package name="VariantAnnotator">
<executable name="VariantAnnotator">
<main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
<resource-bundle file="StingText.properties" />
<dependencies>
<!-- Variant annotator -->
<class>org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator</class>
<class name="org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator" />
<!-- And the annotations -->
<class>org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance</class>
<class>org.broadinstitute.sting.gatk.walkers.annotator.DepthOfCoverage</class>
<class>org.broadinstitute.sting.gatk.walkers.annotator.HomopolymerRun</class>
<class>org.broadinstitute.sting.gatk.walkers.annotator.MappingQualityZero</class>
<class>org.broadinstitute.sting.gatk.walkers.annotator.QualByDepth</class>
<class>org.broadinstitute.sting.gatk.walkers.annotator.RMSMappingQuality</class>
<class>org.broadinstitute.sting.gatk.walkers.annotator.SpanningDeletions</class>
<class name="org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance" />
<class name="org.broadinstitute.sting.gatk.walkers.annotator.DepthOfCoverage" />
<class name="org.broadinstitute.sting.gatk.walkers.annotator.HomopolymerRun" />
<class name="org.broadinstitute.sting.gatk.walkers.annotator.MappingQualityZero" />
<class name="org.broadinstitute.sting.gatk.walkers.annotator.QualByDepth" />
<class name="org.broadinstitute.sting.gatk.walkers.annotator.RMSMappingQuality" />
<class name="org.broadinstitute.sting.gatk.walkers.annotator.SpanningDeletions" />
</dependencies>
</executable>
</package>

12
packages/VariantEval.xml
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@ -1,12 +1,10 @@
<?xml version="1.0" encoding="UTF-8"?>
<package>
<name>VariantEval</name>
<executable>
<name>VariantEval</name>
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<properties>StingText.properties</properties>
<package name="VariantEval">
<executable name="VariantEval">
<main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
<resource-bundle file="StingText.properties" />
<dependencies>
<class>org.broadinstitute.sting.playground.gatk.walkers.varianteval.VariantEvalWalker</class>
<class name="org.broadinstitute.sting.playground.gatk.walkers.varianteval.VariantEvalWalker" />
</dependencies>
</executable>
</package>

12
packages/VariantFiltration.xml
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@ -1,13 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
<package>
<name>VariantFiltration</name>
<executable>
<name>VariantFiltration</name>
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<properties>StingText.properties</properties>
<package name="VariantFiltration">
<executable name="VariantFiltration">
<main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
<resource-bundle file="StingText.properties" />
<dependencies>
<!-- Variant filtration -->
<class>org.broadinstitute.sting.gatk.walkers.filters.VariantFiltrationWalker</class>
<class name="org.broadinstitute.sting.gatk.walkers.filters.VariantFiltrationWalker" />
</dependencies>
</executable>
</package>