hanna ccdb4a0313 General-purpose management of output streams. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1454 348d0f76-0448-11de-a6fe-93d51630548a		2009-08-23 00:56:02 +00:00
..
contexts	Windowed access to the reference.	2009-08-05 16:29:15 +00:00
datasources	fixing a bug where reads in overlapping interval based locus traversals could get assigned to only one of two the regions	2009-08-11 17:50:16 +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	Cleaned division of responsibilities between arguments to map function. Reference has been changed	2009-08-04 21:01:37 +00:00
refdata	make isReference do the right thing	2009-08-19 20:32:29 +00:00
traversals	Windowed access to the reference.	2009-08-05 16:29:15 +00:00
walkers	Added detection of interval files with zero length to the GATK, and removed it from the interval merger walker: this was a critical blocking emergency issue for Eric.	2009-08-21 05:35:49 +00:00
CommandLineExecutable.java	General-purpose management of output streams.	2009-08-23 00:56:02 +00:00
CommandLineGATK.java	Better formatting of available walkers, and only output them along with help. Cleanup JVMUtils.	2009-07-21 22:23:28 +00:00
GATKArgumentCollection.java	Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. *Very*	2009-07-29 16:11:45 +00:00
GenomeAnalysisEngine.java	General-purpose management of output streams.	2009-08-23 00:56:02 +00:00
Reads.java	Better support for specifying read filters to apply directly from the walkers.	2009-07-09 23:59:53 +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