Changes to enable CMake compilation

CMakeLists.txt

@@ -0,0 +1,20 @@
+cmake_minimum_required(VERSION 3.3)
+project(satsuma2)
+
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -lpthread -std=c++14 -O3")
+
+set(SOURCE_FILES_MATCHDUMP kmatch/matchdump.cc kmatch/matchresult.h kmatch/KMatch.h)
+set(SOURCE_FILES_KMATCH kmatch/KMatch.cc kmatch/KMatch.h kmatch/matchresult.h kmatch/KMatch.h)
+set(SOURCE_FILES_MERGEXCORRMATCHES analysis/MergeXCorrMatches.cc base/StringUtil.cc analysis/DNAVector.cc base/FileParser.cc analysis/XCorrDynProg.cc analysis/SequenceMatch.cc util/mutil.cc)
+set(SOURCE_FILES_MATCHESBYFEATURE tools/MatchesByFeature.cc)
+set(SOURCE_FILES_CHAINMATCHES analysis/ChainMatches.cc base/StringUtil.cc analysis/DNAVector.cc base/FileParser.cc analysis/XCorrDynProg.cc analysis/MatchDynProg.cc analysis/SequenceMatch.cc util/mutil.cc)
+set(SOURCE_FILES_SATSUMASYNTENY2 analysis/SatsumaSynteny2.cc analysis/DNAVector.cc base/FileParser.cc util/mutil.cc analysis/CodonTranslate.cc analysis/SeqChunk.cc base/StringUtil.cc analysis/AlignProbability.cc analysis/WorkQueue.cc analysis/MatchDynProg.cc util/SysTime.cc analysis/SequenceMatch.cc analysis/GridSearch.cc)
+set(SOURCE_FILES_HOMOLOGYBYXCORRSLAVE analysis/HomologyByXCorrSlave.cc analysis/ProbTable.cc analysis/DNAVector.cc base/FileParser.cc util/mutil.cc analysis/CrossCorr.cc analysis/CodonTranslate.cc analysis/SeqChunk.cc base/StringUtil.cc analysis/AlignProbability.cc)
+
+add_executable(matchdump ${SOURCE_FILES_MATCHDUMP})
+add_executable(kmatch ${SOURCE_FILES_KMATCH})
+add_executable(MergeXCorrMatches ${SOURCE_FILES_MERGEXCORRMATCHES})
+add_executable(MatchesByFeature ${SOURCE_FILES_MATCHESBYFEATURE})
+add_executable(ChainMatches ${SOURCE_FILES_CHAINMATCHES})
+add_executable(SatsumaSynteny2 ${SOURCE_FILES_SATSUMASYNTENY2})
+add_executable(HomologyByXCorrSlave ${SOURCE_FILES_HOMOLOGYBYXCORRSLAVE})