ebanks 74751a8ed3 -Some minor fixes to get accurate vcf record merging done ... -Improvement to snp genotype concordance test And with that, it looks like I get revision #2000. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2000 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-09 06:40:55 +00:00
..
contexts	Alignment context now supports the idea of skipped bases -- not currently in use	2009-09-12 19:11:38 +00:00
datasources	Added accessors to the rod data sources so that walkers can access the name/file/type triplets for input rods. This is necessary if e.g. you want to create a vcf writer based on all of the samples being input.	2009-11-09 04:25:39 +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	Support for initialize() and onTraversalDone() output from parallelized walkers.	2009-10-26 20:18:31 +00:00
filters	throw an exception if read has no associated read group	2009-10-15 18:11:32 +00:00
io	Support for initialize() and onTraversalDone() output from parallelized walkers.	2009-10-26 20:18:31 +00:00
iterators	a fix for a bug Andrey discovered: in read-based interval traversals we're dupplicating reads in rare cases. The problem was that to accomidate a bug in SAM JDK indexing, we were forced to add one to the stop of our QueryOverlapping() calls to ensure we always got all of the overlapping reads.	2009-11-05 05:26:33 +00:00
refdata	-Some minor fixes to get accurate vcf record merging done	2009-11-09 06:40:55 +00:00
traversals	Reverting rod walkers to use underlying refwalker implementation while we work on ROD2 and reenable the system. Added some serious sparse file parsing to variant eval tests	2009-10-29 01:04:37 +00:00
walkers	Fixed a minor bug where the lodThreshold wasn't being printed in the header.	2009-11-08 16:51:36 +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	adding error log reporting to the GATK, and a stream based output method for the argument collection	2009-10-28 19:56:05 +00:00
GATKArgumentCollection.java	adding error log reporting to the GATK, and a stream based output method for the argument collection	2009-10-28 19:56:05 +00:00
GenomeAnalysisEngine.java	Added accessors to the rod data sources so that walkers can access the name/file/type triplets for input rods. This is necessary if e.g. you want to create a vcf writer based on all of the samples being input.	2009-11-09 04:25:39 +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