Mark DePristo 592f90aaef ActivityProfile now cuts intelligently at the best local minimum when in a larger than max size active region ... -- This new algorithm is essential to properly handle activity profiles that have many large active regions generated from lots of dense variant events. The new algorithm passes unit tests and passes visualize visual inspection of both running on 1000G and NA12878 -- Misc. commenting of the code -- Updated ActiveRegionExtension to include a min active region size -- Renamed ActiveRegionExtension to ActiveRegionTraversalParameters, as it carries more than just the traversal extension now		2013-01-24 13:48:00 -05:00
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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
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java	ActivityProfile now cuts intelligently at the best local minimum when in a larger than max size active region	2013-01-24 13:48:00 -05:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Remove DepthOfCoverage.java because it is no longer public	2013-01-10 11:45:38 -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	Merge branch 'master' of github.com:broadinstitute/gsa-unstable	2013-01-18 15:03:42 -05:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00