David Roazen cdea744b95 Improve -dcov documentation to address recent user confusion ... -Explicitly state that -dcov does not produce an unbiased random sampling from all available reads at each locus, and that instead it tries to maintain an even representation of reads from all alignment start positions (which, of course, is a form of bias) -Recommend -dfrac for users who want a true across-the-board unbiased random sampling		2013-07-02 15:33:28 -04:00
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R	Removed plots generation from the BaseRecalibration software	2013-06-19 14:47:56 -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	Improve -dcov documentation to address recent user confusion	2013-07-02 15:33:28 -04:00
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	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	Update licenses for new PbsEngine* classes	2013-07-01 15:50:20 -04:00
testdata	Somehow the index of exampleDBSNP.vcf was missing	2013-05-28 15:29:43 -04:00