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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alignment	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
commandline	Nearing final BCF commit	2012-06-14 16:42:32 -04:00
gatk	Simple optimizations for BCF2Encoder	2012-06-14 16:42:39 -04:00
jna	Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000.	2012-05-29 11:18:22 -04:00
utils	Optimizations for VCF and BCF2	2012-06-14 16:42:39 -04:00
BaseTest.java	Fix bug in incorrectly reporting relative paths in log	2012-06-14 16:42:37 -04:00
MD5DB.java	Algorithmically faster version of DiffEngine	2012-06-14 16:42:30 -04:00
MD5Mismatch.java	Final updates to integration tests for BCF2	2012-05-24 10:58:59 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	Initial version of clean, fast formatting routines built dynamically from a VCF header	2012-06-14 16:42:30 -04:00