bthomas de9f1f575f Fixing command line parsing to accept negative number arguments. Command line definitions must now start with a letter or underscore; previously, they could start with a digit. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3603 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-21 21:54:31 +00:00
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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	Major bug fixes for the Variant Recalibrator. Covariance matrix values are now allowed to be negative. When probabilities are multiplied together the calculation is done in log space, normalized, then converted back to real valued probabilities. Clustering weights have been changed to only use HapMap and by-1000genomes sites. The -nI argument was removed and now clustering simply runs until convergence. Test cases seem to work best when using just two annotations (QD and SB). More changes are in the works and are being evaluated. Misc fixes to walkers that use RScript due to CentOS changes.	2010-06-18 17:37:11 +00:00
commandline	Fixing command line parsing to accept negative number arguments. Command line definitions must now start with a letter or underscore; previously, they could start with a digit.	2010-06-21 21:54:31 +00:00
gatk	Updating the way reference data is processed, so GATK creates the .fasta.fai and .dict files automatically. If either (or both) don't exist, GATK will create them in the same folder as the fasta file. If it can't write the file, GATK will fail with a message to create them manually.	2010-06-21 21:42:42 +00:00
oneoffprojects	A refactoring / unification of ReadBackedPileup and ReadBackedExtendedEventPileup.	2010-06-20 04:42:26 +00:00
playground	Add -noVerbose flag to stop output of INFO data.	2010-06-18 18:53:35 +00:00
queue/util	Fix for a reflection issue with generic types.	2010-06-16 15:58:38 +00:00
utils	Fixing the error messages thrown with bad interval arguments. I simplified the exception handling and made the messages more verbose.	2010-06-21 21:49:41 +00:00