ebanks 5fdf17fccb Removed the VCF "NS" annotation (which wasn't working for pooled calls anyways) since it's ambiguous and not useful. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2465 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-29 17:30:47 +00:00
..
contexts	UG is now officially in the business of making good SNP calls (as opposed to being hyper-aggressive in its calls and expecting the end-user to filter).	2009-12-16 17:28:09 +00:00
datasources	Temporary hack for Tim Fennell: introduce a sharding strategy that stuffs all data into a single	2009-12-16 21:55:42 +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	Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file	2009-12-04 20:08:41 +00:00
filters	Optimizations:	2009-12-16 21:39:58 +00:00
io	UnifiedGenotyper now works without -varout or -vf set.	2009-12-29 16:46:24 +00:00
iterators	Fixed curiously epic failure in read-backed pileup: size() mismatched the numReads-numDeletions at that locus in the case where includeReadsWithDeletionsAtLoci == false, causing failures including bad output from pileup walker. Also fixed up ValidatingPileup to run with the new ReadBackedPileup instead of just compiling successfully.	2009-12-18 22:52:44 +00:00
refdata	Converter from HapMap chip genotype data to VCF added; HapMapGenotypeROD adjusted to not convert from Hg18 to b36 formatting of contigs	2009-12-28 01:36:08 +00:00
traversals	Completely rewritten duplicate traversal, more free of bugs, with integration tests for count duplicates walker validated on a TCGA hybrid capture lane.	2009-12-28 23:56:49 +00:00
walkers	Removed the VCF "NS" annotation (which wasn't working for pooled calls anyways) since it's ambiguous and not useful.	2009-12-29 17:30:47 +00:00
CommandLineExecutable.java	First revision of command-line argument support for GenotypeWriter. Also, fixed the damn build.	2009-12-20 19:19:23 +00:00
CommandLineGATK.java	Cleanup of the doc system, and introduce Kiran's concept of a detailed summary	2009-12-12 04:04:37 +00:00
GATKArgumentCollection.java	added changes to the code to allow different types of interval merging,	2009-12-23 21:59:14 +00:00
GenomeAnalysisEngine.java	Reads now have new traversal flag: generateExtendedEvents(). Support added to GenomeAnalysisEngine and Walker. This is a silent and transparent framework change that no existing code is going to see. The actual code that makes use of the new flag (which is false by default) will be committed separately...	2009-12-28 19:52:44 +00:00
Reads.java	Reads now have new traversal flag: generateExtendedEvents(). Support added to GenomeAnalysisEngine and Walker. This is a silent and transparent framework change that no existing code is going to see. The actual code that makes use of the new flag (which is false by default) will be committed separately...	2009-12-28 19:52:44 +00:00
WalkerManager.java	Cleanup of the doc system, and introduce Kiran's concept of a detailed summary	2009-12-12 04:04:37 +00:00
package-info.java	Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file	2009-12-04 20:08:41 +00:00