aaron 6313c465fb we want the RMS of the reads qualities not the RMS of the RMS of the read qualities. ... Also the VCF version tag seems to be standardized as VCR. Updated the VCF code. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1447 348d0f76-0448-11de-a6fe-93d51630548a		2009-08-20 21:56:29 +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	A bit of reorganization to help with more flexible output streams. Pushed construction of data	2009-07-29 23:00:15 +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
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	we want the RMS of the reads qualities not the RMS of the RMS of the read qualities.	2009-08-20 21:56:29 +00:00
CommandLineExecutable.java	Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. *Very*	2009-07-29 16:11:45 +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	added the ability to pass in a csv file of ROD triplets (one triplet per line) to the -B option	2009-08-11 22:10:20 +00:00
OutputTracker.java	Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. *Very*	2009-07-29 16:11:45 +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