Mark DePristo 5a5422e4f8 Refactor PerSampleReadStates into a separate class ... -- No longer update the total counts in each per-sample state manager, but instead return delta counts that are updated by the overall ReadStateManager -- One step on the way to improving the underlying representation of the data in PerSampleReadStateManager -- Make LocusIteratorByState final		2013-01-14 16:30:16 -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	Refactor PerSampleReadStates into a separate class	2013-01-14 16:30:16 -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