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gatk-3.8/packages/VariantAnnotator.xml

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Add new 'module' XML tag, that can import modules from supplementary files. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2624 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 09:56:04 +08:00
<?xml version="1.0" encoding="UTF-8"?>
Cleanup and formatting overhaul. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2652 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-22 03:22:56 +08:00
<package name="VariantAnnotator">
<executable name="VariantAnnotator">
<main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
<resource-bundle file="StingText.properties" />
Add new 'module' XML tag, that can import modules from supplementary files. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2624 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 09:56:04 +08:00
<dependencies>
<!-- Variant annotator -->
Cleanup and formatting overhaul. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2652 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-22 03:22:56 +08:00
<class name="org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator" />
updating the package git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3045 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 21:42:31 +08:00
<!-- The interfacess -->
<class name="org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationType" />
<class name="org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation" />
<class name="org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation" />
<class name="org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation" />
<!-- The annotations -->
Include all standard annotations git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4479 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-12 04:52:08 +08:00
<class name="org.broadinstitute.sting.gatk.walkers.annotator.DepthPerAlleleBySample" />
Cleanup and formatting overhaul. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2652 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-22 03:22:56 +08:00
<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" />
Adding HaplotypeScore to the VariantAnnotator package (so it can be used with Firehose) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3171 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 02:37:21 +08:00
<class name="org.broadinstitute.sting.gatk.walkers.annotator.HaplotypeScore" />
Include all standard annotations git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4479 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-12 04:52:08 +08:00
<class name="org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCounts" />
Add new 'module' XML tag, that can import modules from supplementary files. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2624 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 09:56:04 +08:00
</dependencies>
</executable>
</package>