Mark DePristo 9a0dda71d4 BCF2 optimizations ... -- All low-level reads throw IOException instead of catching it directly. This allows us to not try/catch in readByte, improving performance by 5% or so -- Optimize encodeTypeDescriptor with final variables. Avoid using Math.min instead do inline comparison -- Inlined willOverflow directly in its single use		2012-08-09 16:36:18 -04:00
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R	Merged bug fix from Stable into Unstable	2012-08-01 14:35:30 -04:00
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	BCF2 optimizations	2012-08-09 16:36:18 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Removed 'Walker' suffix from packages/GATKEngine.xml that were breaking the packaged release.	2012-07-23 16:32:31 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Hmm, I thought I used the right md5s last time. Let's try again.	2012-08-02 11:25:10 -04:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00