ebanks 01e7b39c8d 1. Don't print out values in filter field of the VCF. ... 2. Fix ratio printouts (for params file) 3. Rename ratio filter's get counts method to avoid confusion; more changes on the way this week. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1616 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-14 21:03:39 +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	Changes to switch Variant Eval over to the new Variation system.	2009-09-14 05:34:33 +00:00
traversals	Framework for ROD walkers -- totally experiment and not working right now	2009-09-12 19:13:15 +00:00
walkers	1. Don't print out values in filter field of the VCF.	2009-09-14 21:03:39 +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