Eric Banks f0bd1b5ae5 Okay, all public->protected dependencies are gone except for the BQSR arguments. I'll need to think through this but should be able to make that work too.		2013-01-08 15:46:32 -05:00
..
R	Fix a nasty bug in reading GATK reports with a single line	2012-09-10 20:14:13 -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	…
doc	…
java	Okay, all public->protected dependencies are gone except for the BQSR arguments. I'll need to think through this but should be able to make that work too.	2013-01-08 15:46:32 -05:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package	2012-12-19 10:25:22 -05:00
perl	Split out contig names from Reference .fai file on white space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz, which does not use tab delimiters)	2012-06-07 16:56:32 -04:00
scala	Moved processing pipelines to private	2013-01-07 14:49:57 -05:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00