Mauricio Carneiro 921eaad33f Generalized the default platform parameter in BQSRv2 ... Parameter wasn't working outside of the BQSR walker. It now takes the information on the recalibration report in other tools (PrintReads for example) and treats all reads as coming from the defined default platform.		2012-07-20 17:29:13 -04:00
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R	GATK Error messages now point to the new website instead of GetSatisfaction.	2012-07-20 17:27:11 -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	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	Generalized the default platform parameter in BQSRv2	2012-07-20 17:29:13 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Removed the "Walker" suffix from all walkers that had it.	2012-07-20 17:27:11 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	GATK Error messages now point to the new website instead of GetSatisfaction.	2012-07-20 17:27:11 -04:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00