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Mark DePristo 14d8afe413 Remove startSearchAt state variable from ActivityProfile 
-- New algorithm will only try to create an active region if there's at least maxREgionSize + propagation distance states in the list.  When that's true, we are guaranteed to actually find a region.  So this algorithm is not only truly correct but as super fast, as we only ever do the search for the end of the region when we will certainly find one, and actually generate a region.
 		2013-01-27 14:10:08 -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
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java Remove startSearchAt state variable from ActivityProfile 2013-01-27 14:10:08 -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 Making metrics a required parameter in MarkDuplicates 2013-01-25 17:49:49 -05:00
testdata Reverting move of BQSR tests to public, as per DR's email 2012-07-19 10:02:05 -04:00