Mauricio Carneiro 5af373a3a1 BQSR with indels integrated! ... * added support to base before deletion in the pileup * refactored covariates to operate on mismatches, insertions and deletions at the same time * all code is in private so original BQSR is still working as usual in public * outputs a molten CSV with mismatches, insertions and deletions, time to play! * barely tested, passes my very simple tests... haven't tested edge cases.		2012-02-09 18:46:45 -05:00
..
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	BQSR with indels integrated!	2012-02-09 18:46:45 -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	Minor manual merge update for List class to Seq interface usage.	2012-02-08 02:24:54 -05:00
testdata	Data Processing Pipeline Test	2011-12-12 00:24:51 -05:00