ebanks 5d85bd9671 By default, VF should ask for deleted bases so that they show up in coverage. ... The Strand filter then needs to ignore those bases when determining bias. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1636 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-16 16:46:09 +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	Missing file	2009-09-12 19:17:09 +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	Always create output files, even if no output was written to them.	2009-09-15 17:58:14 +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	Fix for problem where err stream remapped to output stream in certain cases, (hopefully) completing Matt's hat trick of fail. Thanks, unit tests.	2009-09-16 08:33:56 +00:00
iterators	1) now is tolerant to sloppy cigar strings with 0-length elements (at the price of extra recursive call)	2009-09-09 20:04:04 +00:00
refdata	incremental clean-up and changes for VariantEval, moved DiploidGenotype to a better home, and fixed a spelling error.	2009-09-15 04:48:42 +00:00
traversals	Framework for ROD walkers -- totally experiment and not working right now	2009-09-12 19:13:15 +00:00
walkers	By default, VF should ask for deleted bases so that they show up in coverage.	2009-09-16 16:46:09 +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	Set default value of useLocusIteratorByHanger to FALSE. Otherwise the -LIBH flag is useless and there'd be no wayto "unset" the 'true' value. Old version was (always) using LocusIteratorByHanger. Now default iterator is indeed LocusIteratorByState, and -LIBH will switch back to the old one	2009-09-09 15:09:09 +00:00
GenomeAnalysisEngine.java	Framework for ROD walkers -- totally experiment and not working right now	2009-09-12 19:13:15 +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