hanna 85bc9d3e91 (Hopefully) temporary hack: load contig information by contig name rather than contig id to avoid ... off-by-one errors. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2078 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-18 23:33:27 +00:00
..
contexts	VariantFilteration now accepts a VCF rod in addition to an input geli. It will then annotate this VCF file with filtering information in the INFO field too. --OnlyAnnotate will not write in filtering output	2009-11-10 13:24:58 +00:00
datasources	Command-line arguments for SamReadFilters.	2009-11-10 23:36:17 +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	Command-line arguments for SamReadFilters.	2009-11-10 23:36:17 +00:00
io	Support for initialize() and onTraversalDone() output from parallelized walkers.	2009-10-26 20:18:31 +00:00
iterators	(Hopefully) temporary hack: load contig information by contig name rather than contig id to avoid	2009-11-18 23:33:27 +00:00
refdata	Pileup cleanup; pooled caller v1	2009-11-18 17:03:48 +00:00
traversals	cleanup of the traversal output code	2009-11-12 06:18:10 +00:00
walkers	-Don't annotate allele balance or on-off genotype if there's no genotype data	2009-11-18 22:01:32 +00:00
CommandLineExecutable.java	Command-line arguments for SamReadFilters.	2009-11-10 23:36:17 +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	Fix some problematic command-line argument naming and descriptions.	2009-11-12 02:12:26 +00:00
GenomeAnalysisEngine.java	Take 2, updating picard with bug fix for bam files containing no reads.	2009-11-12 22:52:08 +00:00
Reads.java	Command-line arguments for SamReadFilters.	2009-11-10 23:36:17 +00:00
WalkerManager.java	Allow users to directly specify filters from the command-line, applicable to	2009-11-10 18:40:16 +00:00
package.html	More package-level documentation.	2009-06-17 16:28:45 +00:00