depristo 449a6ba75a Deleting lots of code as part of my cleanup. More classes tagged for removal. Many more walkers have their days numbered. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1885 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-20 12:23:36 +00:00
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contexts	Alignment context now supports the idea of skipped bases -- not currently in use	2009-09-12 19:11:38 +00:00
datasources	Deleting lots of code as part of my cleanup. More classes tagged for removal. Many more walkers have their days numbered.	2009-10-20 12:23:36 +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	Always create output files, even if no output was written to them.	2009-09-15 17:58:14 +00:00
filters	throw an exception if read has no associated read group	2009-10-15 18:11:32 +00:00
io	SAMFileWriters specified as command-line arguments were sometimes incorrectly altering the default short name. Make sure short name is not specified if shortName is not specified but fullName is.	2009-10-09 19:16:46 +00:00
iterators	Deleting lots of code as part of my cleanup. More classes tagged for removal. Many more walkers have their days numbered.	2009-10-20 12:23:36 +00:00
refdata	Reverting previous change.	2009-10-20 00:55:24 +00:00
traversals	memory leak, where the Resource Pool was releasing based on the value and not the key, resulting in the resourceAssignments map growing with each additional shard	2009-10-20 00:39:42 +00:00
walkers	Deleting lots of code as part of my cleanup. More classes tagged for removal. Many more walkers have their days numbered.	2009-10-20 12:23:36 +00:00
CommandLineExecutable.java	Better integrate the @ArgumentCollection into the command-line argument parser. Walkers can now specify their own @ArgumentCollections. Also cleaned up a bit of the CommandLineProgram template method pattern to minimize duplicate code.	2009-09-29 22:23:19 +00:00
CommandLineGATK.java	Update gsadevelopers -> gsahelp.	2009-09-20 23:36:54 +00:00
GATKArgumentCollection.java	Deleting lots of code as part of my cleanup. More classes tagged for removal. Many more walkers have their days numbered.	2009-10-20 12:23:36 +00:00
GenomeAnalysisEngine.java	Added ValidationData analysis type to VariantEvalWalker; this eval takes a GFF file with validated truth data positions (bound to "validation")and calculates the accuracy of the genotype calls bound to "eval".	2009-10-16 15:39:08 +00:00
Reads.java	bug fixes to LIBS and LIBH following ultra-aggressive regression testing across 454, solid, and solexa	2009-09-09 15:36:12 +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