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
..
alignment	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
commandline	Added ability to specify arguments in files via -args/--arg_file	2011-10-24 15:58:34 -04:00
gatk	Revert "First implementation of GATKReportGatherer"	2012-02-08 23:28:55 -05:00
jna	When using bam list mode in HSP deriving VCF name from bam list instead of requiring an additional parameter.	2011-12-16 18:09:25 -05:00
utils	BQSR with indels integrated!	2012-02-09 18:46:45 -05:00
BaseTest.java	Refactor the Pileup Element with regards to indels	2012-01-24 16:07:21 -05:00
MD5DB.java	Merged bug fix from Stable into Unstable	2011-10-13 18:02:06 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	All MD5 mismatches for test are shown	2011-10-04 15:53:52 -07:00