Merge branch 'release/0.6.3-beta'

CMakeLists.txt

@@ -8,7 +8,7 @@ project(octopus)
 
 set(octopus_VERSION_MAJOR 0)
 set(octopus_VERSION_MINOR 6)
-set(octopus_VERSION_PATCH 2)
+set(octopus_VERSION_PATCH 3)
 set(octopus_VERSION_RELEASE beta)
 
 # Get the current working branch

README.md

@@ -43,6 +43,7 @@ $ octopus -R hs37d5.fa -I NA12878.bam -T 1 to MT -o NA12878.octopus.vcf.gz --for
 * Git 2.5 or greater
 * Boost 1.65 or greater
 * htslib 1.4 or greater
+* GMP 5.1.0 or greater
 * CMake 3.9 or greater
 * Optional:
     * Python3 or greater
@@ -56,6 +57,7 @@ $ brew update
 $ brew install git
 $ brew install --with-clang llvm
 $ brew install boost
+$ brew install gmp
 $ brew install cmake
 $ brew tap homebrew/science # required for htslib
 $ brew install htslib
@@ -72,6 +74,7 @@ Depending on your Ubuntu distribution, some requirements can be installed with `
 $ sudo add-apt-repository ppa:ubuntu-toolchain-r/test
 $ sudo apt-get update && sudo apt-get upgrade
 $ sudo apt-get install gcc-7
+$ sudo apt-get install libgmp3-dev
 $ sudo apt-get install git-all
 $ sudo apt-get install python3
 ```

build/cmake/modules/FindGMP.cmake

@@ -0,0 +1,76 @@
+# Try to find the GMP library
+# https://gmplib.org/
+#
+# This module supports requiring a minimum version, e.g. you can do
+#   find_package(GMP 6.0.0)
+# to require version 6.0.0 to newer of GMP.
+#
+# Once done this will define
+#
+#  GMP_FOUND - system has GMP lib with correct version
+#  GMP_INCLUDES - the GMP include directory
+#  GMP_LIBRARIES - the GMP library
+#  GMP_VERSION - GMP version
+#
+# Copyright (c) 2016 Jack Poulson, <jack.poulson@gmail.com>
+# Redistribution and use is allowed according to the terms of the BSD license.
+
+find_path(GMP_INCLUDES NAMES gmp.h PATHS ${GMPlib_ROOT} $ENV{GMPDIR} ${INCLUDE_INSTALL_DIR} PATH_SUFFIXES include)
+
+# Set GMP_FIND_VERSION to 5.1.0 if no minimum version is specified
+if(NOT GMP_FIND_VERSION)
+    if(NOT GMP_FIND_VERSION_MAJOR)
+        set(GMP_FIND_VERSION_MAJOR 5)
+    endif()
+    if(NOT GMP_FIND_VERSION_MINOR)
+        set(GMP_FIND_VERSION_MINOR 1)
+    endif()
+    if(NOT GMP_FIND_VERSION_PATCH)
+        set(GMP_FIND_VERSION_PATCH 0)
+    endif()
+    set(GMP_FIND_VERSION
+        "${GMP_FIND_VERSION_MAJOR}.${GMP_FIND_VERSION_MINOR}.${GMP_FIND_VERSION_PATCH}")
+endif()
+
+message(STATUS "GMP_INCLUDES=${GMP_INCLUDES}")
+if(GMP_INCLUDES)
+    # Since the GMP version macros may be in a file included by gmp.h of the form
+    # gmp-.*[_]?.*.h (e.g., gmp-x86_64.h), we search each of them.
+    file(GLOB GMP_HEADERS "${GMP_INCLUDES}/gmp.h" "${GMP_INCLUDES}/gmp-*.h")
+    foreach(gmp_header_filename ${GMP_HEADERS})
+        file(READ "${gmp_header_filename}" _gmp_version_header)
+        string(REGEX MATCH
+            "define[ \t]+__GNU_MP_VERSION[ \t]+([0-9]+)" _gmp_major_version_match
+            "${_gmp_version_header}")
+        if(_gmp_major_version_match)
+            set(GMP_MAJOR_VERSION "${CMAKE_MATCH_1}")
+            string(REGEX MATCH "define[ \t]+__GNU_MP_VERSION_MINOR[ \t]+([0-9]+)"
+                _gmp_minor_version_match "${_gmp_version_header}")
+            set(GMP_MINOR_VERSION "${CMAKE_MATCH_1}")
+            string(REGEX MATCH "define[ \t]+__GNU_MP_VERSION_PATCHLEVEL[ \t]+([0-9]+)"
+                _gmp_patchlevel_version_match "${_gmp_version_header}")
+            set(GMP_PATCHLEVEL_VERSION "${CMAKE_MATCH_1}")
+            set(GMP_VERSION
+                ${GMP_MAJOR_VERSION}.${GMP_MINOR_VERSION}.${GMP_PATCHLEVEL_VERSION})
+        endif()
+    endforeach()
+
+    # Check whether found version exists and exceeds the minimum requirement
+    if(NOT GMP_VERSION)
+        set(GMP_VERSION_OK FALSE)
+        message(STATUS "GMP version was not detected")
+    elseif(${GMP_VERSION} VERSION_LESS ${GMP_FIND_VERSION})
+        set(GMP_VERSION_OK FALSE)
+        message(STATUS "GMP version ${GMP_VERSION} found in ${GMP_INCLUDES}, "
+            "but at least version ${GMP_FIND_VERSION} is required")
+    else()
+        set(GMP_VERSION_OK TRUE)
+    endif()
+endif()
+
+find_library(GMP_LIBRARIES gmp PATHS ${GMPlib_ROOT} $ENV{GMPDIR} ${LIB_INSTALL_DIR} PATH_SUFFIXES lib)
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(GMP DEFAULT_MSG
+    GMP_INCLUDES GMP_LIBRARIES GMP_VERSION_OK)
+mark_as_advanced(GMP_INCLUDES GMP_LIBRARIES)