Karthik Gururaj 7180c392af 1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the ... SSE compilation warning. 2. Added code to dynamically select between AVX, SSE4.2 and normal C++ (in that order) 3. Created multiple files to compile with different compilation flags: avx_function_prototypes.cc is compiled with -xAVX while sse_function_instantiations.cc is compiled with -xSSE4.2 flag. 4. Added jniClose() and support in Java (HaplotypeCaller, PairHMMLikelihoodCalculationEngine) to call this function at the end of the program. 5. Removed debug code, kept assertions and profiling in C++ 6. Disabled OpenMP for now.		2014-01-20 08:03:42 -08:00
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alignment	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
commandline	Add ability to specify min/max required/recommended values for numeric arguments in the @Argument annotation	2013-12-18 18:09:08 -05:00
gatk	Better documentation for ReadClippingStats walker	2014-01-01 14:26:26 -05:00
jna	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
queue	fix a (ugly) weird error from last commit that changed all the scala files to end with MoleculoPipeline.scala	2013-11-18 11:44:24 -05:00
tools	New VCF engine arguments to specify an alternate IndexCreator	2013-12-03 13:31:02 -05:00
utils	1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the	2014-01-20 08:03:42 -08:00