Mark DePristo 0384ce5d34 Simple optimizations for BCF2Encoder ... -- Inline encodeString that doesn't go via List<Byte> intermediate -- Inline encodeString that uses byte[] directly so that we can go from Allele.getBytes() => BCF2 -- Fast paths for Atomic Float and Atomic Integer values avoiding intermediate list creation -- Final UG integration test update		2012-06-14 16:42:39 -04:00
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datasources	GATK tests use public/testdata not /humgen/ as much as possible	2012-05-24 10:58:58 -04:00
downsampling	Make downsampler classes themselves generic (instead of just the Downsampler interface)	2012-06-13 16:43:39 -04:00
executive	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
filters	GATK tests use public/testdata not /humgen/ as much as possible	2012-05-24 10:58:58 -04:00
iterators	Removing extended event related unit tests	2012-04-02 14:40:36 -04:00
refdata	Bugfixes and testdata cleanup	2012-05-24 13:26:05 -04:00
report	GATK tests use public/testdata not /humgen/ as much as possible	2012-05-24 10:58:58 -04:00
samples	Added function to get founders IDs in SampleDB	2012-04-25 12:49:36 -04:00
traversals	First pass of the asynchronous block loader.	2011-11-18 15:02:59 -05:00
walkers	Simple optimizations for BCF2Encoder	2012-06-14 16:42:39 -04:00
EngineFeaturesIntegrationTest.java	Nearing final BCF commit	2012-06-14 16:42:32 -04:00
GenomeAnalysisEngineUnitTest.java	Allow processing of empty intervals, but warn user when this case is encountered.	2011-10-28 12:12:14 -04:00
WalkerManagerUnitTest.java	Moving more tools over to use the standard VC arg collection. Also, while I'm in there, I removed all of the empty references to @Requires given that it's no longer relevant.	2011-08-10 12:20:18 -04:00