gatk-3.8/packages/QualityScoresRecalibration.xml

<?xml version="1.0" encoding="UTF-8"?>
<package name="QualityScoresRecalibration">
  <executable name="QualityScoresRecalibration">
    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
    <resource-bundle file="StingText.properties" />
    <dependencies>
      <!-- Quality scores recalibration -->
      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker" />
      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker" />
      <!-- Recalibration Covariates -->
      <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>
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="QualityScoresRecalibration">`
			`<executable name="QualityScoresRecalibration">`
			`<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>`
			`<!-- Quality scores recalibration -->`
A few more bug fixes based on extended testing. Sorry, Eric. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2656 348d0f76-0448-11de-a6fe-93d51630548a 2010-01-22 06:12:16 +08:00			`<class name="org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker" />`
			`<class name="org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker" />`
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			`<!-- Recalibration Covariates -->`
A few more bug fixes based on extended testing. Sorry, Eric. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2656 348d0f76-0448-11de-a6fe-93d51630548a 2010-01-22 06:12:16 +08:00			`<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" />`
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>`