Merge pull request #56 from gymreklab/mlamkin7-update-to-cmake

Update to Cmake

Author: mlamkin7

.gitignore

@@ -1,3 +1,4 @@
+build/
 Makefile
 Makefile.in
 aclocal.m4

CMakeLists.txt

@@ -0,0 +1,59 @@
+cmake_minimum_required(VERSION 3.7)
+
+include(ExternalProject)
+
+#set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+#add_compile_options(-Werror)
+
+list(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake)
+
+# set the project name
+project(chips VERSION 2.1)
+configure_file(chipsConfig.h.in chipsConfig.h)
+
+# specify the C++ standard
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD_REQUIRED True)
+
+ExternalProject_Add(zlib
+        PREFIX ${CMAKE_BINARY_DIR}/thirdparty/zlib
+        GIT_REPOSITORY "https://github.com/madler/zlib.git"
+        GIT_TAG "v1.2.8"
+        UPDATE_COMMAND ""
+        BUILD_IN_SOURCE 1
+        CONFIGURE_COMMAND ${CMAKE_BINARY_DIR}/thirdparty/zlib/src/zlib/configure --prefix=${CMAKE_BINARY_DIR}/thirdparty/zlib --static
+        INSTALL_DIR ${CMAKE_BINARY_DIR}/thirdparty/zlib
+        LOG_DOWNLOAD 1
+        LOG_INSTALL 1
+        )
+ExternalProject_Add(htslib
+        PREFIX ${CMAKE_BINARY_DIR}/thirdparty/htslib
+        GIT_REPOSITORY "https://github.com/samtools/htslib.git"
+        GIT_TAG "1.3.1"
+        UPDATE_COMMAND ""
+        BUILD_IN_SOURCE 1
+        CONFIGURE_COMMAND ""
+        BUILD_COMMAND make
+        INSTALL_COMMAND make install prefix=${CMAKE_BINARY_DIR}/thirdparty/htslib
+        LOG_DOWNLOAD 1
+        )
+
+include_directories(${CMAKE_CURRENT_SOURCE_DIR})
+include_directories(${CMAKE_BINARY_DIR}/thirdparty/zlib/include)
+set(zlib_static ${CMAKE_BINARY_DIR}/thirdparty/zlib/lib/libz.a)
+set(htslib_static ${CMAKE_BINARY_DIR}/thirdparty/htslib/lib/libhts.a)
+include_directories(${CMAKE_BINARY_DIR}/thirdparty/htslib/include)
+add_dependencies(htslib zlib)
+
+add_subdirectory(ChIPs)
+
+# add the executable
+add_executable(chips src/main.cpp)
+
+target_compile_features(chips PRIVATE cxx_range_for)
+target_include_directories(chips PUBLIC "${PROJECT_BINARY_DIR}")
+target_link_libraries(chips ChIPs pthread)
+install(TARGETS chips DESTINATION bin)
+
+add_dependencies(htslib zlib)
+add_dependencies(ChIPs htslib)

ChIPs/CMakeLists.txt

@@ -0,0 +1,4 @@
+file(GLOB SOURCES *.cpp *.h *.hpp)
+add_library(ChIPs ${SOURCES})
+target_link_libraries(ChIPs ${htslib_static} ${zlib_static})
+target_include_directories(ChIPs PUBLIC "${PROJECT_BINARY_DIR}")

src/bam_io.cpp ChIPs/bam_io.cppsrc/bam_io.cpp renamed to ChIPs/bam_io.cpp

@@ -21,7 +21,7 @@
 #define bam_ins_size(b)  (b)->core.isize;
 #include "htslib/sam.h"
 
-#include "src/common.h"
+#include "common.h"
 
 // htslib encodes each base using a 4 bit integer
 // This array converts each integer to its corresponding base
@@ -171,7 +171,8 @@ class BamAlignment {
   bool AddStringTag(const char tag[2], const std::string& value){
     if (HasTag(tag))
       return false;
-    return (bam_aux_append(b_, tag, 'Z', value.size()+1, (uint8_t*)value.c_str()) == 0);
+    bam_aux_append(b_, tag, 'Z', value.size()+1, (uint8_t*)value.c_str());
+    return true;
   }
 
   bool GetCharTag(const char tag[2], char& value) const {

src/bam_io.h ChIPs/bam_io.hsrc/bam_io.h renamed to ChIPs/bam_io.h

@@ -1,6 +1,6 @@
-#include "src/bingenerator.h"
-#include "src/ref_genome.h"
-#include "src/common.h"
+#include "bingenerator.h"
+#include "ref_genome.h"
+#include "common.h"
 
 #include <sstream>
 #include <iostream>

src/bingenerator.cpp ChIPs/bingenerator.cppsrc/bingenerator.cpp renamed to ChIPs/bingenerator.cpp

@@ -1,7 +1,7 @@
 #ifndef SRC_BINGENERATOR_H__
 #define SRC_BINGENERATOR_H__
 
-#include "src/options.h"
+#include "options.h"
 #include <vector>
 #include <map>
 

src/bingenerator.h ChIPs/bingenerator.hsrc/bingenerator.h renamed to ChIPs/bingenerator.h

@@ -4,7 +4,8 @@
 #include <iostream>
 #include <sstream>
 
-#include "src/common.h"
+#include "common.h"
+#include "chipsConfig.h"
 
 using namespace std;
 
@@ -27,8 +28,8 @@ void PrintMessageDieOnError(const string& msg, MSGTYPE msgtype) {
     errx(1, "Invalid message type. This should never happen");
   }
   stringstream ss;
-  ss  << "[" << PROGRAM_NAME
-      << "-" << _GIT_VERSION << "] " << typestring << msg << endl;
+  ss << "[chips-" << chips_VERSION_MAJOR << "." << chips_VERSION_MINOR << "]"
+     << typestring << msg << endl;
   cerr << ss.str();
 
   if (msgtype == M_ERROR) {

src/common.cpp ChIPs/common.cppsrc/common.cpp renamed to ChIPs/common.cpp

@@ -1,4 +1,4 @@
-#include "src/fragment.h"
+#include "fragment.h"
 
 Fragment::Fragment(const std::string& _chrom, const std::int32_t& _start, const std::size_t& _length, const float& _score){
   chrom = _chrom;