depristo 65e9dcf5b7 Fully operational version of the new genotype likelihoods class. (1) Much cleaner interface. Now explicitly stores likelihoods, priors, and posteriors in separate arrays indexed by an enum, (2) no longer can be used to make calls, it relies on SSGGenotypeCall to order the likelihoods, calculate best to ref, etc, this is just for calculating genotype likelihoods now; (3) Now performs extensive error checking with validate() to ensure the system is behaving properly. (4) fixed incorrect treatment of N bases, which we being counted against everyone (5) likely found a stats bug in which heterozyosity was being applied incorrectly to the genotype priors ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1382 348d0f76-0448-11de-a6fe-93d51630548a		2009-08-05 01:00:55 +00:00
..
contexts	Cleaned division of responsibilities between arguments to map function. Reference has been changed	2009-08-04 21:01:37 +00:00
datasources	Cleaned division of responsibilities between arguments to map function. Reference has been changed	2009-08-04 21:01:37 +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	Made sure all RODs have a (good) toString() method - and use it in the Venn walker. (thanks, Mark)	2009-07-30 14:53:27 +00:00
traversals	Cleaned division of responsibilities between arguments to map function. Reference has been changed	2009-08-04 21:01:37 +00:00
walkers	Fully operational version of the new genotype likelihoods class. (1) Much cleaner interface. Now explicitly stores likelihoods, priors, and posteriors in separate arrays indexed by an enum, (2) no longer can be used to make calls, it relies on SSGGenotypeCall to order the likelihoods, calculate best to ref, etc, this is just for calculating genotype likelihoods now; (3) Now performs extensive error checking with validate() to ensure the system is behaving properly. (4) fixed incorrect treatment of N bases, which we being counted against everyone (5) likely found a stats bug in which heterozyosity was being applied incorrectly to the genotype priors	2009-08-05 01:00:55 +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	A bit of reorganization to help with more flexible output streams. Pushed construction of data	2009-07-29 23:00:15 +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