aaron 5a3bd50537 adding error log reporting to the GATK, and a stream based output method for the argument collection ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1926 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-28 19:56:05 +00:00
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contexts	Alignment context now supports the idea of skipped bases -- not currently in use	2009-09-12 19:11:38 +00:00
datasources	Almost ready to stop doing eagar decoding; waiting on Eric	2009-10-27 15:28:05 +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	throw an exception if read has no associated read group	2009-10-15 18:11:32 +00:00
io	Support for initialize() and onTraversalDone() output from parallelized walkers.	2009-10-26 20:18:31 +00:00
iterators	Deleting lots of code as part of my cleanup. More classes tagged for removal. Many more walkers have their days numbered.	2009-10-20 12:23:36 +00:00
refdata	intermediate commit for some changes in the Variation system, so Eric can go ahead with his changes. Everything is pretty set, but the Variation interface could use a convenience method that joins all the alternate alleles.	2009-10-23 06:31:15 +00:00
traversals	a fix for traverse dupplicates bug: GSA-202. Also removed some debugging output from FastaAltRef walker	2009-10-26 20:18:55 +00:00
walkers	removed the GenotypesBacked interface, which is currently unused. Also cleaned up some documentation lines	2009-10-28 18:08:14 +00:00
CommandLineExecutable.java	Better integrate the @ArgumentCollection into the command-line argument parser. Walkers can now specify their own @ArgumentCollections. Also cleaned up a bit of the CommandLineProgram template method pattern to minimize duplicate code.	2009-09-29 22:23:19 +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	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
GenomeAnalysisEngine.java	Enabling correct high-performance ROD walker and moved VariantEval over to it. Performance improvements in variantEval in general. See wiki for full description	2009-10-20 23:31:13 +00:00
Reads.java	bug fixes to LIBS and LIBH following ultra-aggressive regression testing across 454, solid, and solexa	2009-09-09 15:36:12 +00:00
WalkerManager.java	Better formatting of available walkers, and only output them along with help. Cleanup JVMUtils.	2009-07-21 22:23:28 +00:00
package.html	More package-level documentation.	2009-06-17 16:28:45 +00:00