Compiles on Mac OS now and added edit distance in utils dir

Author: Andreas Grigorjew

.gitignore

@@ -0,0 +1,5 @@
+emerald
+cmake_install.cmake
+CMakeCache.txt
+Makefile
+CMakeFiles/

CMakeLists.txt

@@ -0,0 +1,27 @@
+cmake_minimum_required(VERSION 3.9)
+# Get project name from folder name
+get_filename_component(ProjectId ${CMAKE_CURRENT_SOURCE_DIR} NAME)
+string(REPLACE " " "_" ProjectId ${ProjectId})
+project(${ProjectId})
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}")
+# all .cpp files
+set(SOURCES src/main.cpp src/alpha_safe_paths.cpp src/optimal_paths.cpp src/safety_windows.cpp)
+add_executable(${ProjectId} ${SOURCES})
+# compiler flags for debugging
+if (APPLE)
+    set(CMAKE_CXX_FLAGS "-O3 -openmp")
+else()
+    set(CMAKE_CXX_FLAGS "-O3 -fopenmp")
+endif()
+
+# GMP
+find_package(GMP REQUIRED)
+# if .h files are in other folder?
+include_directories(./ ${GMP_INCLUDE_DIR})
+target_link_libraries(${ProjectId} ${GMP_LIBRARY})
+# OpenMP
+#find_package(OpenMP REQUIRED)
+#target_link_libraries(${ProjectId} OpenMP::OpenMP_CXX)
+# runnable output file
+set_target_properties(${ProjectId} PROPERTIES OUTPUT_NAME "emerald")

FindGMP.cmake

@@ -0,0 +1,18 @@
+set(GMP_PREFIX "" CACHE PATH "path ")
+find_path(GMP_INCLUDE_DIR gmp.h gmpxx.h 
+    PATHS ${GMP_PREFIX}/include /usr/include /usr/local/include )
+find_library(GMP_LIBRARY NAMES gmp libgmp 
+    PATHS ${GMP_PREFIX}/lib /usr/lib /usr/local/lib)
+if(GMP_INCLUDE_DIR AND GMP_LIBRARY)
+    get_filename_component(GMP_LIBRARY_DIR ${GMP_LIBRARY} PATH)
+    set(GMP_FOUND TRUE)
+endif()
+if(GMP_FOUND)
+   if(NOT GMP_FIND_QUIETLY)
+      MESSAGE(STATUS "Found GMP: ${GMP_LIBRARY}")
+   endif()
+elseif(GMP_FOUND)
+   if(GMP_FIND_REQUIRED)
+      message(FATAL_ERROR "Could not find GMP")
+   endif()
+endif()

README.md

@@ -35,5 +35,5 @@ Run with $\alpha$ = 0.75 and $\Delta$ = 8.
 ```
 Use edit distance with only optimal alignments and 100%-safety and multi threading:
 ```
-./emerald -f example.fasta -a 1 -d 0 --costmat edit_distance.txt --gapcost 1 --startgap 0 --threads 8
+./emerald -f example.fasta -a 1 -d 0 --costmat utils/edit_distance.txt --gapcost 1 --startgap 0 --threads 8
 ```

src/safety_windows.h

@@ -1,3 +1,4 @@
+#include <unordered_map>
 #include <vector>
 #include <gmpxx.h>
 

utils/edit_distance.txt

@@ -0,0 +1,20 @@
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