init: LinearFold-C

CMakeLists.txt

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+#cmake_minimum_required(VERSION 3.6)
+project(fastcky)
+
+if($ENV{CXX})
+  set(CMAKE_CXX_COMPILER $ENV{CXX} CACHE FILEPATH "CXX Compiler")
+endif()
+if($ENV{CC})
+  set(CMAKE_CC_COMPILER $ENV{CC} CACHE FILEPATH "CC Compiler")
+endif()
+
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -O3")
+
+#set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -lprofiler")
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -ltcmalloc -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free")
+
+set(BEAMCKYPAR_SOURCE
+        beamckypar.cpp
+        beamckypar.h
+        fastcky_w.h
+        utility.h
+        cxxopts.hpp)
+
+add_executable(linearfold ${BEAMCKYPAR_SOURCE})

README.md

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+RNA Sequence Parser for Structure Prediction
+============================================
+
+The source code of the LinearFold project, a linear-time RNA secondary structure prediction algorithm.
+
+### Linear-Time Prediction for RNA Secondary Structures
+
+Paper:
+LinearFold: Linear-Time Prediction of RNA Secondary Structures
+Dezhong Deng, Kai Zhao, David Hendrix, David Mathews, Liang Huang
+doi: https://doi.org/10.1101/263509
+
+#### To Compile
+LinearFold can be compiled with ```cmake``` with following commands:
+
+```
+mkdir build
+cd build
+cmake ..
+make linearfold
+```
+
+Note that there are two external libraries stated in ```CMakeLists.txt``` file:
+
+1. ```-lprofiler``` is from Google Performance Tools, and is used to profile the parser, which is turned __off__ by default.
+2. ```-ltcmalloc``` is also from Google Performance Tools, which replaces the default ```malloc``` from ```glibc``` and can bring ~5% speedup.
+
+
+#### To Run
+The LinearFold parser can be run with:
+```
+linearfold sequence_file [beam_size]
+```
+
+The default beam_size is infinite.
+