ebanks 89771fef05 -Use read.getReadGroup() ... -Add another filter for read groups for Chris git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1835 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-14 18:08:32 +00:00
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contexts	Alignment context now supports the idea of skipped bases -- not currently in use	2009-09-12 19:11:38 +00:00
datasources	Note to myself: do 'ant clean' now and then or old versions of the code that suddenly became invalid will stick around. The world is not perfect, and neither is automatic dependency resolution.	2009-09-21 17:40:52 +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	-use the getReadGroup() function that was added to picard for us	2009-10-12 01:39:32 +00:00
io	SAMFileWriters specified as command-line arguments were sometimes incorrectly altering the default short name. Make sure short name is not specified if shortName is not specified but fullName is.	2009-10-09 19:16:46 +00:00
iterators	A big fix for MergingSamRecordIterator, where we weren't correctly handling the comparisons of SAMRecords correctly (we weren't applying the new reference index first, so sometimes the MT contig would be ID 23, sometimes 24 in different records).	2009-10-02 19:35:35 +00:00
refdata	Merge both versions of the Sequenom assay design maker: use Jared's base code and add in indels. [Jared, this still emits the same output for SNPs as your original version)	2009-10-14 17:11:45 +00:00
traversals	Framework for ROD walkers -- totally experiment and not working right now	2009-09-12 19:13:15 +00:00
walkers	-Use read.getReadGroup()	2009-10-14 18:08:32 +00:00
CommandLineExecutable.java	Better integrate the @ArgumentCollection into the command-line argument parser. Walkers can now specify their own @ArgumentCollections. Also cleaned up a bit of the CommandLineProgram template method pattern to minimize duplicate code.	2009-09-29 22:23:19 +00:00
CommandLineGATK.java	Update gsadevelopers -> gsahelp.	2009-09-20 23:36:54 +00:00
GATKArgumentCollection.java	Better integrate the @ArgumentCollection into the command-line argument parser. Walkers can now specify their own @ArgumentCollections. Also cleaned up a bit of the CommandLineProgram template method pattern to minimize duplicate code.	2009-09-29 22:23:19 +00:00
GenomeAnalysisEngine.java	GSA-182: Adding support for BED interval files.	2009-10-06 02:45:31 +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