rpoplin 6bb864da2a More misc cleanup. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2191 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-30 22:29:07 +00:00
..
contexts	ReadBackedPileup in all its glory. Documented, aligned with the output of LocusIteratorByState, and caching common outputs for performance	2009-11-25 20:54:44 +00:00
datasources	An iterator for Eric to use when injecting his new wrapping reads -- a stopgap solution for getting additional caching	2009-11-27 22:25:52 +00:00
examples	Cleaned division of responsibilities between arguments to map function. Reference has been changed	2009-08-04 21:01:37 +00:00
executive	Support for initialize() and onTraversalDone() output from parallelized walkers.	2009-10-26 20:18:31 +00:00
filters	Changed the format of the recalibration csv file slightly so that it is easier to load the file into something like R and look at the values of the covariates.	2009-11-30 17:55:23 +00:00
io	Support for initialize() and onTraversalDone() output from parallelized walkers.	2009-10-26 20:18:31 +00:00
iterators	Completing the optimization started by Matt: we now wrap SAMRecords and SAMReadGroupRecords with our own versions which cache oft-used variables (e.g. platform, readString, strand flag). All walkers automagically get this speedup since the wrapping occurs in the engine.	2009-11-30 17:39:29 +00:00
refdata	Completing the optimization started by Matt: we now wrap SAMRecords and SAMReadGroupRecords with our own versions which cache oft-used variables (e.g. platform, readString, strand flag). All walkers automagically get this speedup since the wrapping occurs in the engine.	2009-11-30 17:39:29 +00:00
traversals	ReadBackedPileup in all its glory. Documented, aligned with the output of LocusIteratorByState, and caching common outputs for performance	2009-11-25 20:54:44 +00:00
walkers	More misc cleanup.	2009-11-30 22:29:07 +00:00
CommandLineExecutable.java	Command-line arguments for SamReadFilters.	2009-11-10 23:36:17 +00:00
CommandLineGATK.java	adding error log reporting to the GATK, and a stream based output method for the argument collection	2009-10-28 19:56:05 +00:00
GATKArgumentCollection.java	Fix some problematic command-line argument naming and descriptions.	2009-11-12 02:12:26 +00:00
GenomeAnalysisEngine.java	Added dbSNP sanity check to CountCovariates. If the mismatch rate is too low at dbSNP sites it warns the user that the dbSNP file is suspicious. Added option in CountCovariates and TableRecalibration to ignore read group id's and collapse them together. Also, If the read group is null the walkers no long crash with NullPointerException but instead warn the user the read group and platform are defaulting to some values. Default window size in MinimumNQSCovariate is 5 (two bases in either direction) based on rereading of Chris's analysis.	2009-11-24 16:16:44 +00:00
Reads.java	Command-line arguments for SamReadFilters.	2009-11-10 23:36:17 +00:00
WalkerManager.java	Allow users to directly specify filters from the command-line, applicable to	2009-11-10 18:40:16 +00:00
package.html	More package-level documentation.	2009-06-17 16:28:45 +00:00