aaron 3c2ae55859 changes for the genotype overhaul. Lots of changes focusing on the output side, from single sample genotyper to the output file formats like GLF and geli. Of note the genotype formats are still emitting posteriors as likelihoods; this is the way we've been doing it but it may change soon. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1529 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-04 05:31:15 +00:00
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contexts	Require each filter or feature to declare whether or not they want mapping quality zero reads in the alignment context	2009-08-31 03:31:37 +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	Add an indel rod which represents the initial point of the indel only	2009-09-02 19:32:29 +00:00
traversals	Windowed access to the reference.	2009-08-05 16:29:15 +00:00
walkers	changes for the genotype overhaul. Lots of changes focusing on the output side, from single sample genotyper to the output file formats like GLF and geli. Of note the genotype formats are still emitting posteriors as likelihoods; this is the way we've been doing it but it may change soon.	2009-09-04 05:31:15 +00:00
CommandLineExecutable.java	General-purpose management of output streams.	2009-08-23 00:56:02 +00:00
CommandLineGATK.java	Force columnSpacing to be at least one. We need a general-purpose, working tool for outputting columnar data to a PrintStream; will add JIRA.	2009-08-25 19:54:54 +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