Eric Banks de56134579 Fixed up and refactored what seems to be a useful private tool to create simulated reads around a VCF. ... It didn't completely work before (it was hard-coded for a particular long-lost data set) but it should work now. Since I thought that it might prove useful to others, I moved it to protected and added integration tests. GERALDINE: NEW TOOL ALERT!		2014-01-15 13:49:31 -05:00
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R	Something changed with the ggtitle syntax in the latest version of ggplot2.	2013-08-14 14:40:03 -04:00
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	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
java	Updated SAMPileup codec and pileup-related docs	2014-01-14 09:14:16 -05:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	ValidatingPileup was renamed to CheckPileup	2013-02-15 11:56:19 -05:00
perl	Fixing the liftover script to not require strict VCF header validation.	2013-11-07 09:02:17 -05:00
scala	Merge remote-tracking branch 'origin/master' into mf_new_RBP	2013-12-19 10:42:20 -05:00
testdata	Fixed up and refactored what seems to be a useful private tool to create simulated reads around a VCF.	2014-01-15 13:49:31 -05:00