aaron 2b7d39035a switched over the FastaAlternateReferenceWalker to the Variation system ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1726 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-25 16:09:43 +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	Note to myself: do 'ant clean' now and then or old versions of the code that suddenly became invalid will stick around. The world is not perfect, and neither is automatic dependency resolution.	2009-09-21 17:40:52 +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	Always create output files, even if no output was written to them.	2009-09-15 17:58:14 +00:00
filters	Filter for reads with missing read groups so we can safely assume all reads have valid read groups	2009-09-24 16:10:26 +00:00
io	Let Picard specify the default compression level.	2009-09-23 19:01:48 +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	switched over the FastaAlternateReferenceWalker to the Variation system	2009-09-25 16:09:43 +00:00
traversals	Framework for ROD walkers -- totally experiment and not working right now	2009-09-12 19:13:15 +00:00
walkers	switched over the FastaAlternateReferenceWalker to the Variation system	2009-09-25 16:09:43 +00:00
CommandLineExecutable.java	Make unpackList public static so that Doug can use it in the scatter/gather framework.	2009-09-21 15:32:49 +00:00
CommandLineGATK.java	Update gsadevelopers -> gsahelp.	2009-09-20 23:36:54 +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