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Package all walkers in org/broadinstitute/sting/gatk/walkers directory in release. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4702 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-11-18 02:33:45 +00:00
parent 9942f436b4
commit 9f356b6cd0
3 changed files with 7 additions and 25 deletions
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2
java/src/org/broadinstitute/sting/gatk/examples/papergenotyper/package-info.java
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@ -1,4 +1,4 @@
/**
* @help.display.name The GATK paper's Bayesian genotyper
*/
package org.broadinstitute.sting.playground.gatk.walkers.papergenotyper;
package org.broadinstitute.sting.gatk.examples.papergenotyper;

26
packages/GenomeAnalysisTK.xml
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@ -4,33 +4,15 @@
<executable name="GenomeAnalysisTK">
<main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
<resource-bundle file="StingText.properties" />
<modules>
<module file="QualityScoresRecalibration.xml" />
<module file="VariantRecalibration.xml" />
<module file="LocalRealignmentAroundIndels.xml" />
<module file="UnifiedGenotyper.xml" />
<module file="VariantEval.xml" />
<module file="VariantFiltration.xml" />
<module file="VariantAnnotator.xml" />
<module file="IndelGenotyper.xml" />
</modules>
<dependencies>
<!-- Core walkers -->
<package name="org.broadinstitute.sting.gatk.walkers.**" />
<!-- Filters -->
<package name="org.broadinstitute.sting.gatk.filters" />
<!-- Tribble codecs -->
<package name="org.broad.tribble.*" />
<!-- Basic qc walkers -->
<class name="org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker" />
<class name="org.broadinstitute.sting.gatk.walkers.coverage.DoCOutputMultiplexer" />
<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" />
<!-- Other misc walkers -->
<class name="org.broadinstitute.sting.gatk.walkers.variantutils.CombineVariants" />
<class name="org.broadinstitute.sting.gatk.walkers.VariantsToVCF" />
<!-- Workaround - depend on the logger impl required by JEXL -->
<package name="org.apache.commons.logging.impl" />
</dependencies>
</executable>
<modules>

4
perl/runReleaseSanityCheck.pl
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@ -19,11 +19,11 @@ $command = "$command_prefix -T DepthOfCoverage -I /humgen/gsa-hpprojects/GATK/da
run($command, $dry);
print "Executing CountCovariatesWholeExome...";
$command = "$command_prefix -T CountCovariates -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.bam -L /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/whole_exome_agilent_designed_120.targets.chr1.interval_list -standard -OQ -recalFile /dev/null -XL chr1:1,000,000-247179187";
$command = "$command_prefix -T CountCovariates -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.bam -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -L /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/whole_exome_agilent_designed_120.targets.chr1.interval_list -standard -OQ -recalFile /dev/null -XL chr1:1,000,000-247179187";
run($command, $dry);
print "Executing CountCovariatesWholeGenome...";
$command = "$command_prefix -T CountCovariates -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.bam -L chr1:1,900,000-2,000,000 -standard -OQ -recalFile /dev/null";
$command = "$command_prefix -T CountCovariates -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.bam -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -L chr1:1,900,000-2,000,000 -standard -OQ -recalFile /dev/null";
run($command, $dry);
print "Executing TableRecalibratorWholeExome...";