rpoplin 062b316881 Better Exception message when can't find annotation value in variant recalibrator. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3434 348d0f76-0448-11de-a6fe-93d51630548a		2010-05-25 21:15:50 +00:00
..
alignment	BaseUtils has more clear distinction between byte and char routines. All char routines are @Depreciated now. Please use bytes. Better organization of reverse(), now in Utils not BaseUtils.	2010-05-20 14:05:13 +00:00
analyzecovariates	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
commandline	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
gatk	Variant Recalibrator now makes use of a prior on known/novel status as well as on allele frequency spectrum. The VariantOptimizer walker now clusters with all variants but gives more weight to knowns / hapmap / 1KG / MQ1 sites. The weights are all optional command line arguments. We no longer assign default values to annotations that are malformed. The walkers will crash with exception so as to not cover up potential issues. We only produce titv-less clusters now, and so the titv argument in VO was removed and the WithoutTiTv string that gets added to the cluster file is removed. The wiki is updated to show new example commands.	2010-05-25 21:08:31 +00:00
oneoffprojects	A downsampling validator. Compares the generated pileup passed in from the alignment context to the reads,	2010-05-23 21:49:54 +00:00
playground	Better Exception message when can't find annotation value in variant recalibrator.	2010-05-25 21:15:50 +00:00
utils	Fixed UG parallelization bug. Better integration test to catch this in the future.	2010-05-25 21:03:45 +00:00