ebanks 1e8dcc30da -dbSNP rod should not implement VariantBackedByGenotype since dbsnp records have no genotype data ... -added code to cache the allele list so it didn't need to get recomputed each time it was requested. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2260 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-04 14:56:48 +00:00
..
contexts	fixes for VariantAnnotations and second bases. Misc. removal of failing (and unstable) integration tests that require rereview	2009-12-02 15:41:35 +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	- Optimized implementation of -byReadGroup in DoCWalker	2009-12-02 03:39:24 +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	Improved performance of deletion-free pileup and added mapping-quality-zero-free pileup convenience method.	2009-12-01 04:50:47 +00:00
refdata	-dbSNP rod should not implement VariantBackedByGenotype since dbsnp records have no genotype data	2009-12-04 14:56:48 +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	You can now use the -exp flag to tell the Genotyper to include experimental annotations when it calls out to VariantAnnotator.	2009-12-04 04:45:05 +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	Un-reinventing the wheel. --sleep argument removed.	2009-12-02 20:19:28 +00:00
GenomeAnalysisEngine.java	Un-reinventing the wheel. --sleep argument removed.	2009-12-02 20:19:28 +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