rpoplin 79c4cc1db7 AnalyzeAnnotations now breaks out titv by calls in hapmap and also plots true positive rates. Any RODs passed in whose name starts with 'truth' is considered to be the truth set. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2726 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-28 21:41:23 +00:00
..
arguments	Better handling of enums by the command-line argument system.	2010-01-20 21:36:46 +00:00
contexts	added a method to AlignmentContext called hasExceededMaxPileup, which you can use to determine if the current site exceeded the maximum pileup size (reads were dropped). Added this as a check to unified genotyper according to Eric's instructions, and added the plumbing to the engine.	2010-01-27 05:17:01 +00:00
datasources	added a method to AlignmentContext called hasExceededMaxPileup, which you can use to determine if the current site exceeded the maximum pileup size (reads were dropped). Added this as a check to unified genotyper according to Eric's instructions, and added the plumbing to the engine.	2010-01-27 05:17:01 +00:00
examples	Completed my documentation responsibilities - based on Mark's reasonable assignment and not the one Matt made up while on Meth.	2009-12-13 04:13:30 +00:00
executive	First successful test of new sharding system prototype. Can traverse over reads from a single	2010-01-15 03:35:55 +00:00
filters	Updated the min mapping quality and min base quality defaults to be 10 in both cases (and updated all integration tests) as suggested by Mark.	2010-01-03 21:31:04 +00:00
io	Better handling of enums by the command-line argument system.	2010-01-20 21:36:46 +00:00
iterators	AnalyzeAnnotations seems to be popular so I've rewritten the guts to be easier to extend and maintain.	2010-01-27 19:30:31 +00:00
refdata	Lots of changes; all to do something relatively minor.	2010-01-28 21:06:56 +00:00
traversals	AnalyzeAnnotations now breaks out titv by calls in hapmap and also plots true positive rates. Any RODs passed in whose name starts with 'truth' is considered to be the truth set.	2010-01-28 21:41:23 +00:00
walkers	Lots of changes; all to do something relatively minor.	2010-01-28 21:06:56 +00:00
CommandLineExecutable.java	Looks bigger than it is:	2010-01-15 00:14:35 +00:00
CommandLineGATK.java	Update our error messages to point to getsatisfaction.com/gsa.	2010-01-27 19:16:28 +00:00
GenomeAnalysisEngine.java	First successful test of new sharding system prototype. Can traverse over reads from a single	2010-01-15 03:35:55 +00:00
Reads.java	changes to intelligently log overflowing locus pile-ups.	2010-01-20 08:09:48 +00:00
WalkerManager.java	Bug fix for help text / version number - help text retriever was crashing in the debugger if help text hadn't been built.	2010-01-20 19:18:19 +00:00
package-info.java	Put a major.minor version into the GATK Javadoc for reading. Also,	2010-01-15 21:48:30 +00:00