Mauricio Carneiro ec9920b04f Updating the SAM TAG for Original Alignment Start to "OP" ... per Mark's recommendation to reuse the Indel Realigner tag that made it to the SAM spec. The Alignment end tag is still "OE" as there is no official tag to reuse.		2012-01-27 08:51:39 -05:00
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R	queueJobReport now compresses PDF when running R 2.13+.	2012-01-10 17:32:30 -05:00
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	Updating the SAM TAG for Original Alignment Start to "OP"	2012-01-27 08:51:39 -05:00
packages	Revved Picard to incorporate tfennell's AsyncSAMFileWriter.	2011-12-06 10:37:42 -05:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	another small bug with the file extension.	2012-01-24 16:14:35 -05:00
testdata	Data Processing Pipeline Test	2011-12-12 00:24:51 -05:00