Commit d3dc5272 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 2.3.14+dfsg

parent d41fc64e

.travis.yml

+8 −4
Original line number Diff line number Diff line
@@ -27,10 +27,13 @@ env: 
  - METHOD_TEST=tests/hbltests/libv3/aBSREL.wbf

  - METHOD_TEST=tests/hbltests/libv3/BUSTED.wbf

  - METHOD_TEST=tests/hbltests/libv3/LEISR.wbf

  - METHOD_TEST=tests/hbltests/libv3/BGM.wbf



language: c++



compiler: 

  - gcc

  - clang



addons:

  apt:
@@ -39,17 +42,18 @@ addons: 
        - ubuntu-toolchain-r-test

        - george-edison55-precise-backports

    packages:

        - g++-6

        - gcc-6

        - g++-7

        - gcc-7



install:

  - if [ "$CXX" = "g++" ]; then export CXX="g++-6" CC="gcc-6"; fi

  - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi

  - cmake . 

  - make HYPHYMP

  - make HYPHYGTEST



script: 

  - export OMP_NUM_THREADS=4

  - export OMP_NUM_THREADS=8

  - export LD_LIBRARY_PATH=/usr/local/clang/lib:$LD_LIBRARY_PATH

  - ./HYPHYGTEST

  - ./HYPHYMP LIBPATH=`pwd`/res/ tests/hbltests/libv3/math.bf

  - ./HYPHYMP LIBPATH=`pwd`/res/ tests/hbltests/libv3/iofunctions.bf

CMakeLists.txt

+21 −9
Original line number Diff line number Diff line
@@ -20,9 +20,9 @@ macro(PCL_CHECK_FOR_SSE3) 
  include(CheckCXXSourceRuns)

  set(CMAKE_REQUIRED_FLAGS)



  if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)

  if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_CXX_COMPILER_ID MATCHES "Clang")

      set(CMAKE_REQUIRED_FLAGS "-msse3")

  endif(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)

  endif(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_CXX_COMPILER_ID MATCHES "Clang")



  check_cxx_source_runs("

      #include <pmmintrin.h>
@@ -46,9 +46,9 @@ macro(PCL_CHECK_FOR_AVX) 
  include(CheckCXXSourceRuns)

  set(CMAKE_REQUIRED_FLAGS)



  if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)

  if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_CXX_COMPILER_ID MATCHES "Clang")

      set(CMAKE_REQUIRED_FLAGS "-march=corei7-avx -mtune=corei7-avx")

  endif(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)

  endif(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_CXX_COMPILER_ID MATCHES "Clang")



  check_cxx_source_runs("

      #include <immintrin.h>
@@ -71,6 +71,7 @@ endmacro(PCL_CHECK_FOR_AVX) 
set(CMAKE_MODULE_PATH cmake)

set(HYPHY_VERSION 2.1)





#-------------------------------------------------------------------------------

# setup the files we'll be using

#-------------------------------------------------------------------------------
@@ -94,7 +95,6 @@ set(DEFAULT_WARNING_FLAGS "-w") 
set(DEFAULT_DEBUG_WARNING_FLAGS "-Wall -Wno-int-to-pointer-cast -Wno-conversion-null -Wno-sign-compare -Wno-maybe-uninitialized")







if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX)

    execute_process(

        COMMAND ${CMAKE_CXX_COMPILER} -dumpversion
@@ -175,6 +175,14 @@ if(NOT DEFINED DEFAULT_WARNING_FLAGS) 
    set(DEFAULT_WARNING_FLAGS "")

endif(NOT DEFINED DEFAULT_WARNING_FLAGS)



include (CheckLibraryExists)



CHECK_LIBRARY_EXISTS( "libamdlibm.so" "amd_log" "" HAS_AMD_LIBM)

if(HAS_AMD_LIBM)

    set(DEFAULT_LINK_FLAGS "${DEFAULT_LINK_FLAGS} -lamdlibm")

    add_definitions(-D__USEAMDLOG__)

endif(HAS_AMD_LIBM)





#-------------------------------------------------------------------------------

# OpenMP support
@@ -188,8 +196,12 @@ endif(NOT ${OPENMP_FOUND}) 
#-------------------------------------------------------------------------------

# default installation prefix

#-------------------------------------------------------------------------------

set(INSTALL_PREFIX /usr/local CACHE PATH "Installation prefix")

set(CMAKE_INSTALL_PREFIX ${INSTALL_PREFIX} CACHE INTERNAL "Installation prefix" FORCE)

if(NOT DEFINED CMAKE_INSTALL_PREFIX)

    set(CMAKE_INSTALL_PREFIX "/usr/local" CACHE PATH "Installation prefix")

endif()

if(NOT DEFINED INSTALL_PREFIX)

    set(INSTALL_PREFIX ${CMAKE_INSTALL_PREFIX} CACHE INTERNAL "Installation prefix" FORCE)

endif()

if(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")

    set(DEFAULT_LIBRARIES pthread)

else(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")

res/TemplateBatchFiles/BGM.bf

+384 −224

File changed.

Preview size limit exceeded, changes collapsed.

res/TemplateBatchFiles/CleanStopCodons.bf

+2 −0
Original line number Diff line number Diff line
@@ -153,6 +153,8 @@ for (sequenceIndex = 0; sequenceIndex < all64.species; sequenceIndex = sequenceI 
		GetDataInfo (siteInfo, all64, sequenceIndex, siteIndex);

		siteInfo1 = stopCodonTemplate*siteInfo;

		siteInfo2 = nonStopCodonTemplate*siteInfo;

		

		

		if (siteInfo1[0]>0 && siteInfo2[0] == 0)

		{

			sitesWithDeletions[siteIndex] = 1;