aaron b401929e41 incremental clean-up and changes for VariantEval, moved DiploidGenotype to a better home, and fixed a spelling error. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1624 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-15 04:48:42 +00:00
..
contexts	Alignment context now supports the idea of skipped bases -- not currently in use	2009-09-12 19:11:38 +00:00
datasources	Missing file	2009-09-12 19:17:09 +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	General-purpose management of output streams.	2009-08-23 00:56:02 +00:00
filters	Major: allow genotyper to optionally output in 1KG format, including outputting the samples in which indels are found.	2009-07-23 19:53:51 +00:00
io	General-purpose management of output streams.	2009-08-23 00:56:02 +00:00
iterators	1) now is tolerant to sloppy cigar strings with 0-length elements (at the price of extra recursive call)	2009-09-09 20:04:04 +00:00
refdata	incremental clean-up and changes for VariantEval, moved DiploidGenotype to a better home, and fixed a spelling error.	2009-09-15 04:48:42 +00:00
traversals	Framework for ROD walkers -- totally experiment and not working right now	2009-09-12 19:13:15 +00:00
walkers	incremental clean-up and changes for VariantEval, moved DiploidGenotype to a better home, and fixed a spelling error.	2009-09-15 04:48:42 +00:00
CommandLineExecutable.java	General WalkerTest framework. Includes some minor changes to GATK core to enable creation of true command-line like GATK modules in the code. Extensive first-pass tests for SSG	2009-09-04 19:13:37 +00:00
CommandLineGATK.java	General WalkerTest framework. Includes some minor changes to GATK core to enable creation of true command-line like GATK modules in the code. Extensive first-pass tests for SSG	2009-09-04 19:13:37 +00:00
GATKArgumentCollection.java	Set default value of useLocusIteratorByHanger to FALSE. Otherwise the -LIBH flag is useless and there'd be no wayto "unset" the 'true' value. Old version was (always) using LocusIteratorByHanger. Now default iterator is indeed LocusIteratorByState, and -LIBH will switch back to the old one	2009-09-09 15:09:09 +00:00
GenomeAnalysisEngine.java	Framework for ROD walkers -- totally experiment and not working right now	2009-09-12 19:13:15 +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