aaron 8453676b71 added a method to AlignmentContext called hasExceededMaxPileup, which you can use to determine if the current site exceeded the maximum pileup size (reads were dropped). Added this as a check to unified genotyper according to Eric's instructions, and added the plumbing to the engine. ... Also deleted the FixBamSortOrder package that isn't used anymore. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2701 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-27 05:17:01 +00:00
..
Aligner.xml	Cleanup and formatting overhaul.	2010-01-21 19:22:56 +00:00
AnalyzeCovariates.xml	A few more bug fixes based on extended testing. Sorry, Eric.	2010-01-21 22:12:16 +00:00
CreatePackager.xsl	Add new 'release' task to push releases into a shared directory and the website.	2010-01-26 22:50:20 +00:00
FindContaminatingReadGroups.xml	Cleanup and formatting overhaul.	2010-01-21 19:22:56 +00:00
GATK-Picard.xml	A few more bug fixes based on extended testing. Sorry, Eric.	2010-01-21 22:12:16 +00:00
GATKResources.xml	Cleanup and formatting overhaul.	2010-01-21 19:22:56 +00:00
GenomeAnalysisTK.xml	Add new 'release' task to push releases into a shared directory and the website.	2010-01-26 22:50:20 +00:00
LocalRealignmentAroundIndels.xml	Updated the package to use RealignerTargetCreator. Also, removed IndelGenotyper since it's still experimental.	2010-01-27 03:45:15 +00:00
PicardPrivate.xml	Cleanup and formatting overhaul.	2010-01-21 19:22:56 +00:00
QualityScoresRecalibration.xml	A few more bug fixes based on extended testing. Sorry, Eric.	2010-01-21 22:12:16 +00:00
UnifiedGenotyper.xml	Cleanup and formatting overhaul.	2010-01-21 19:22:56 +00:00
VCFValidator.xml	Cleanup and formatting overhaul.	2010-01-21 19:22:56 +00:00
VariantAnnotator.xml	Cleanup and formatting overhaul.	2010-01-21 19:22:56 +00:00
VariantEval.xml	Cleanup and formatting overhaul.	2010-01-21 19:22:56 +00:00
VariantFiltration.xml	Temporary solution: add the commons logging implementation to the VariantFiltration package. Downstream solution is described in GSA-262.	2010-01-23 01:46:18 +00:00