ebanks 5dbba6711c Lots of changes: (I'll send email out in a sec) ... 1) Moved various disparate concordance / set splitting functionalities to a new parent tool which works like VariantFiltration (i.e. people can write various modules that fit inside and can be run though it). 2) Fixed up argument parsing in VariantFiltration to use key=value format so we don't accidentally mox up values (like I had been doing). 3) Have indel rod print samples git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1540 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-07 01:12:09 +00:00
..
contexts	-Renamed rodVariants to RodGeliText	2009-09-04 18:40:43 +00:00
datasources	change to make build work	2009-09-03 13:43:10 +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	General-purpose management of output streams.	2009-08-23 00:56:02 +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
io	General-purpose management of output streams.	2009-08-23 00:56:02 +00:00
iterators	High performance LocusIterator implementation. Now with greatly reduced memory impact and 2x (and more potentially) speed ups of raw locus iteration. General performance improvements to SSG with empirical probs. You can enable high-performance locus iteration with the -LIBS arg. It's still testing but passes validing pileup.	2009-09-03 03:06:25 +00:00
refdata	Lots of changes: (I'll send email out in a sec)	2009-09-07 01:12:09 +00:00
traversals	Windowed access to the reference.	2009-08-05 16:29:15 +00:00
walkers	Lots of changes: (I'll send email out in a sec)	2009-09-07 01:12:09 +00:00
CommandLineExecutable.java	General WalkerTest framework. Includes some minor changes to GATK core to enable creation of true command-line like GATK modules in the code. Extensive first-pass tests for SSG	2009-09-04 19:13:37 +00:00
CommandLineGATK.java	General WalkerTest framework. Includes some minor changes to GATK core to enable creation of true command-line like GATK modules in the code. Extensive first-pass tests for SSG	2009-09-04 19:13:37 +00:00
GATKArgumentCollection.java	High performance LocusIterator implementation. Now with greatly reduced memory impact and 2x (and more potentially) speed ups of raw locus iteration. General performance improvements to SSG with empirical probs. You can enable high-performance locus iteration with the -LIBS arg. It's still testing but passes validing pileup.	2009-09-03 03:06:25 +00:00
GenomeAnalysisEngine.java	added a flag, maximum_reads_at_locus, shortName "mrl", which limits the number of reads we add to the locusByHanger. In some bam files misalignment produces pile-ups of 750K or more reads. We now limit this to the default of 100K reads.	2009-09-01 04:21:58 +00:00
Reads.java	added a flag, maximum_reads_at_locus, shortName "mrl", which limits the number of reads we add to the locusByHanger. In some bam files misalignment produces pile-ups of 750K or more reads. We now limit this to the default of 100K reads.	2009-09-01 04:21:58 +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