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Mark DePristo 2c38310868 Create LIBS using new AlignmentStateMachine infrastructure 
-- Optimizations to AlignmentStateMachine
-- Properly count deletions.  Added unit test for counting routines
-- AlignmentStateMachine.java is no longer recursive
-- Traversals now use new LIBS, not the old one
 		2013-01-11 15:17:17 -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 Create LIBS using new AlignmentStateMachine infrastructure 2013-01-11 15:17:17 -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 Licensing update -- batch #2 2013-01-11 13:38:11 -05:00
testdata Reverting move of BQSR tests to public, as per DR's email 2012-07-19 10:02:05 -04:00