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‎.gitignore‎

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‎Makefile‎

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UNAME_S := $(shell uname -s)
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SRC = src/colord
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ifeq ($(UNAME_S),Darwin)
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CC=/usr/local/bin/g++-10
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CFLAGS = -Wall -O3 -std=c++17 -static-libgcc -static-libstdc++ -pthread
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CLINK = -Wall -O3 -std=c++17 -static-libgcc -static-libstdc++ -lpthread
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CFLAGS_KMC = -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11
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CLINK_KMC = -lm -static -O3 -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11
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else
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CC=g++
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CFLAGS = -Wall -O3 -std=c++17 -static -Wl,--whole-archive -lstdc++fs -lpthread -Wl,--no-whole-archive
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CLINK = -Wall -O3 -std=c++17 -static -Wl,--whole-archive -lstdc++fs -lpthread -Wl,--no-whole-archive
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CFLAGS_KMC = -Wall -O3 -m64 -static-libgcc -static-libstdc++ -fopenmp -pthread -std=c++11
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CLINK_KMC = -lm -fopenmp -static-libgcc -static-libstdc++ -O3 -pthread -std=c++11
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endif
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BIN_DIR = bin
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OBJS = \
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$(SRC)/utils.o \
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$(SRC)/timer.o \
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$(SRC)/stats_collector.o \
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$(SRC)/reads_sim_graph.o \
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$(SRC)/quality_coder.o \
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$(SRC)/quality_coder_impl.o \
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$(SRC)/pooled_threads.o \
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$(SRC)/main.o \
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$(SRC)/in_reads.o \
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$(SRC)/id_coder.o \
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$(SRC)/filter_kmers.o \
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$(SRC)/entr_header.o \
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$(SRC)/encoder.o \
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$(SRC)/dna_coder.o \
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$(SRC)/decompression.o \
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$(SRC)/info.o \
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$(SRC)/count_kmers.o \
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$(SRC)/compression.o \
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$(SRC)/basic_coder.o \
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$(SRC)/arg_parse.o \
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$(SRC)/archive.o \
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$(SRC)/reference_genome.o \
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$(SRC)/libs/edlib/edlib.o \
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$(SRC)/libs/kmc_api/kmc_file.o \
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$(SRC)/libs/kmc_api/kmer_api.o \
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$(SRC)/libs/kmc_api/mmer.o
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COBJS = \
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$(SRC)/libs/md5/md5.o
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ifeq ($(UNAME_S),Darwin)
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LIBS = \
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$(SRC)/libs/zlib/libz.mac.a \
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$(SRC)/libs/mimalloc/libmimalloc.mac.a \
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$(SRC)/libs/count_kmers/libfiltering_kmc.mac.a \
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$(SRC)/libs/count_kmers/libbz2.1.0.5.dylib
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LIB_FILTERING_KMC = $(SRC)/libs/count_kmers/libfiltering_kmc.mac.a
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else
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LIBS = \
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$(SRC)/libs/zlib/libz.a \
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$(SRC)/libs/mimalloc/libmimalloc.a \
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$(SRC)/libs/count_kmers/libfiltering_kmc.a \
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$(SRC)/libs/count_kmers/libbz2.a
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LIB_FILTERING_KMC = $(SRC)/libs/count_kmers/libfiltering_kmc.a
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endif
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$(BIN_DIR)/colord: $(OBJS) $(COBJS) $(LIB_FILTERING_KMC)
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-mkdir -p $(BIN_DIR)
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$(CC) $(CLINK) -o $@ $^ $(LIBS)
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$(OBJS): %.o: %.cpp
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$(CC) $(CFLAGS) -I $(SRC)/libs/zlib -I $(SRC)/libs/kmc_api -I $(SRC)/libs/edlib -I $(SRC)/libs/CLI11 -c $< -o $@
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$(COBJS): %.o: %.c
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$(CC) $(CFLAGS) -I $(SRC)/libs/zlib -I $(SRC)/libs/kmc_api -I $(SRC)/libs/edlib -I $(SRC)/libs/CLI11 -c $< -o $@
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KMC_MAIN_DIR = src/filtering-KMC
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KMC_OBJS = \
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$(KMC_MAIN_DIR)/kmer_counter.o \
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$(KMC_MAIN_DIR)/mmer.o \
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$(KMC_MAIN_DIR)/mem_disk_file.o \
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$(KMC_MAIN_DIR)/rev_byte.o \
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$(KMC_MAIN_DIR)/bkb_writer.o \
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$(KMC_MAIN_DIR)/cpu_info.o \
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$(KMC_MAIN_DIR)/bkb_reader.o \
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$(KMC_MAIN_DIR)/fastq_reader.o \
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$(KMC_MAIN_DIR)/timer.o \
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$(KMC_MAIN_DIR)/develop.o \
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$(KMC_MAIN_DIR)/kb_completer.o \
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$(KMC_MAIN_DIR)/kb_storer.o \
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$(KMC_MAIN_DIR)/kmer.o \
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$(KMC_MAIN_DIR)/splitter.o \
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$(KMC_MAIN_DIR)/kb_collector.o
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ifeq ($(UNAME_S),Darwin)
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RADULS_OBJS =
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else
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RADULS_OBJS = \
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$(KMC_MAIN_DIR)/raduls_sse2.o \
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$(KMC_MAIN_DIR)/raduls_sse41.o \
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$(KMC_MAIN_DIR)/raduls_avx2.o \
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$(KMC_MAIN_DIR)/raduls_avx.o
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endif
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$(KMC_OBJS): %.o: %.cpp
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$(CC) $(CFLAGS_KMC) -c $< -o $@
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$(KMC_MAIN_DIR)/raduls_sse2.o: $(KMC_MAIN_DIR)/raduls_sse2.cpp
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$(CC) $(CFLAGS_KMC) -msse2 -c $< -o $@
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$(KMC_MAIN_DIR)/raduls_sse41.o: $(KMC_MAIN_DIR)/raduls_sse41.cpp
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$(CC) $(CFLAGS_KMC) -msse4.1 -c $< -o $@
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$(KMC_MAIN_DIR)/raduls_avx.o: $(KMC_MAIN_DIR)/raduls_avx.cpp
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$(CC) $(CFLAGS_KMC) -mavx -c $< -o $@
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$(KMC_MAIN_DIR)/raduls_avx2.o: $(KMC_MAIN_DIR)/raduls_avx2.cpp
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$(CC) $(CFLAGS_KMC) -mavx2 -c $< -o $@
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$(LIB_FILTERING_KMC): $(KMC_OBJS) $(RADULS_OBJS)
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-mkdir -p $(BIN_DIR)
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ar rcs $@ $^
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clean:
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-rm -f $(SRC)/*.o
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-rm -f $(SRC)/libs/edlib/edlib.o
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-rm -f $(SRC)/libs/kmc_api/kmc_file.o
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-rm -f $(SRC)/libs/kmc_api/kmer_api.o
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-rm -f $(SRC)/libs/kmc_api/mmer.o
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-rm -f $(KMC_MAIN_DIR)/*.o
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-rm -f $(LIB_FILTERING_KMC)
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-rm -rf bin
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all: $(BIN_DIR)/colord

‎colord.sln‎

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Microsoft Visual Studio Solution File, Format Version 12.00
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# Visual Studio Version 16
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VisualStudioVersion = 16.0.30002.166
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MinimumVisualStudioVersion = 10.0.40219.1
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Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "colord", "src\colord\colord.vcxproj", "{DC5AEB6F-C197-42B7-98E0-E0E1397A0619}"
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EndProject
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Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "filtering_kmc", "src\filtering-KMC\kmer_counter.vcxproj", "{8C8B90DA-28B7-4D82-81F3-C0E7CE52D59F}"
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EndProject
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Global
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GlobalSection(SolutionConfigurationPlatforms) = preSolution
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Debug|x64 = Debug|x64
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Debug|x86 = Debug|x86
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Debug-decomp|x64 = Debug-decomp|x64
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Debug-decomp|x86 = Debug-decomp|x86
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Release - Decomp|x64 = Release - Decomp|x64
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Release - Decomp|x86 = Release - Decomp|x86
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Release|x64 = Release|x64
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Release|x86 = Release|x86
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Relesase - Decompress|x64 = Relesase - Decompress|x64
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Relesase - Decompress|x86 = Relesase - Decompress|x86
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EndGlobalSection
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GlobalSection(ProjectConfigurationPlatforms) = postSolution
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{DC5AEB6F-C197-42B7-98E0-E0E1397A0619}.Debug|x64.ActiveCfg = Debug|x64
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{DC5AEB6F-C197-42B7-98E0-E0E1397A0619}.Debug|x64.Build.0 = Debug|x64
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{DC5AEB6F-C197-42B7-98E0-E0E1397A0619}.Debug|x86.ActiveCfg = Debug|Win32
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{DC5AEB6F-C197-42B7-98E0-E0E1397A0619}.Debug|x86.Build.0 = Debug|Win32
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{DC5AEB6F-C197-42B7-98E0-E0E1397A0619}.Debug-decomp|x64.ActiveCfg = Debug-decomp|x64
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{DC5AEB6F-C197-42B7-98E0-E0E1397A0619}.Release - Decomp|x64.ActiveCfg = Release - Decomp|x64
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{DC5AEB6F-C197-42B7-98E0-E0E1397A0619}.Release - Decomp|x64.Build.0 = Release - Decomp|x64
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{DC5AEB6F-C197-42B7-98E0-E0E1397A0619}.Release - Decomp|x86.ActiveCfg = Release - Decomp|Win32
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{DC5AEB6F-C197-42B7-98E0-E0E1397A0619}.Release - Decomp|x86.Build.0 = Release - Decomp|Win32
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{DC5AEB6F-C197-42B7-98E0-E0E1397A0619}.Release|x64.ActiveCfg = Release|x64
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{DC5AEB6F-C197-42B7-98E0-E0E1397A0619}.Release|x64.Build.0 = Release|x64
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{DC5AEB6F-C197-42B7-98E0-E0E1397A0619}.Release|x86.ActiveCfg = Release|Win32
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{DC5AEB6F-C197-42B7-98E0-E0E1397A0619}.Relesase - Decompress|x64.ActiveCfg = Relesase - Decompress|x64
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{DC5AEB6F-C197-42B7-98E0-E0E1397A0619}.Relesase - Decompress|x86.ActiveCfg = Relesase - Decompress|Win32
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{DC5AEB6F-C197-42B7-98E0-E0E1397A0619}.Relesase - Decompress|x86.Build.0 = Relesase - Decompress|Win32
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{8C8B90DA-28B7-4D82-81F3-C0E7CE52D59F}.Debug|x64.ActiveCfg = Debug|x64
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EndGlobalSection
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GlobalSection(SolutionProperties) = preSolution
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HideSolutionNode = FALSE
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EndGlobalSection
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GlobalSection(ExtensibilityGlobals) = postSolution
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SolutionGuid = {3D0D8E63-21D2-466B-9B28-A2DAD3988562}
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EndGlobalSection
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EndGlobal

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