ebanks 4366ce16e0 Made sure all RODs have a (good) toString() method - and use it in the Venn walker. (thanks, Mark) ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1339 348d0f76-0448-11de-a6fe-93d51630548a		2009-07-30 14:53:27 +00:00
..
datasources	Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. *Very*	2009-07-29 16:11:45 +00:00
examples	First step in replacing the Hello, World! document. Revamped the HelloWalker and checked it into the source tree, created a special build file for it, and added it to the packaging tool.	2009-06-30 21:59:54 +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	Added the interator to SAMDataSource to prevent seeing dupplicate reads, only in a byReads traversal. The iterator discards any reads in the current interval that would have been seen in the previous interval.	2009-07-25 22:36:29 +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	A bit of reorganization to help with more flexible output streams. Pushed construction of data	2009-07-29 23:00:15 +00:00
walkers	A bit of reorganization to help with more flexible output streams. Pushed construction of data	2009-07-29 23:00:15 +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
LocusContext.java	Fixed genome loc to be immutable, the only way to now change it's values is through the GenomeLocParser.	2009-06-30 19:17:24 +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