gatk-3.8

History

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
..
src/org/broadinstitute/sting	1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the	2014-01-20 08:03:42 -08:00
test/org/broadinstitute/sting	Allow for additional input data to be used in the VQSR for clustering but don't carry it forward into the output VCF file.	2014-01-02 14:46:04 -05:00

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

src/org/broadinstitute/sting

1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the

2014-01-20 08:03:42 -08:00

test/org/broadinstitute/sting

Allow for additional input data to be used in the VQSR for clustering but don't carry it forward into the output VCF file.

2014-01-02 14:46:04 -05:00