aaron 3a487dd64e little fixes; also fixed a tyPo ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1662 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-18 22:38:51 +00:00
..
contexts	Modifications:	2009-09-09 15:49:52 +00:00
examples	Update naming for consistency.	2009-06-30 22:03:21 +00:00
gatk	little fixes; also fixed a tyPo	2009-09-18 22:38:51 +00:00
indels	change paths to new ones	2009-07-24 07:28:43 +00:00
piecemealannotator	Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.	2009-07-08 18:49:08 +00:00
somaticcoverage	Cleanup: GATKEngine no longer needs to be lazy loaded, b/c the plugin directory no longer exists.	2009-07-21 18:50:51 +00:00
tools	Very early, half-baked version. All it can do right now is to take two SAM files with end1 and end2 individual single-end alignmnets from a pair-end run and spit out a "paired" BAM file that contains ONLY properly paired ends (both ends align uniquely && both ends align to the same chromosome && the ends align in proper orientation). Insert size is currently not used (and not set in the output). Unpaired/unmapped reads are NOT transferred into the output bam. For the pairs that do get written, the output is (should be) standard-conforming: all flags are properly set and mate pair information is correct.	2009-09-16 18:38:18 +00:00
utils	A little piece that PairMaker needs in order to compile ;)	2009-09-16 19:17:40 +00:00