Many small changes

convert/bin/.gitignore

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+*
+!.gitignore

convert/makefile

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+#COMPILER MODE C++11
+CXX=g++ -std=c++11
+
+
+#create folders
+dummy_build_folder_bin := $(shell mkdir -p bin)
+dummy_build_folder_obj := $(shell mkdir -p obj)
+
+#COMPILER & LINKER FLAGS
+CXXFLAG=-g
+LDFLAG=-g
+
+#COMMIT TRACING
+COMMIT_VERS=$(shell git rev-parse --short HEAD)
+COMMIT_DATE=$(shell git log -1 --format=%cd --date=short)
+CXXFLAG+= -D__COMMIT_ID__=\"$(COMMIT_VERS)\"
+CXXFLAG+= -D__COMMIT_DATE__=\"$(COMMIT_DATE)\"
+
+#DYNAMIC LIBRARIES
+DYN_LIBS=-lz -lpthread -lbz2 -llzma -lcurl -lcrypto
+
+HFILE=$(shell find src -name *.h)
+CFILE=$(shell find src -name *.cpp)
+OFILE=$(shell for file in `find src -name *.cpp`; do echo obj/$$(basename $$file .cpp).o; done)
+VPATH=$(shell for file in `find src -name *.cpp`; do echo $$(dirname $$file); done)
+
+NAME=$(shell basename $(CURDIR))
+BFILE=bin/SHAPEIT5_$(NAME)
+EXEFILE=bin/SHAPEIT5_$(NAME)_static
+
+#CONDITIONAL PATH DEFINITON
+system: DYN_LIBS=-lz -lpthread -lbz2 -llzma
+system: HTSSRC=/usr/local
+system: HTSLIB_INC=$(HTSSRC)/include/htslib
+system: HTSLIB_LIB=$(HTSSRC)/lib/libhts.a
+system: BOOST_INC=/usr/include
+system: BOOST_LIB_IO=/usr/lib/x86_64-linux-gnu/libboost_iostreams.a
+system: BOOST_LIB_PO=/usr/lib/x86_64-linux-gnu/libboost_program_options.a
+system: BOOST_LIB_SE=/usr/lib/x86_64-linux-gnu/libboost_serialization.a
+system: $(BFILE)
+
+desktop: HTSSRC=../..
+desktop: HTSLIB_INC=$(HTSSRC)/htslib
+desktop: HTSLIB_LIB=$(HTSSRC)/htslib/libhts.a
+desktop: BOOST_INC=/usr/include
+desktop: BOOST_LIB_IO=/usr/local/lib/libboost_iostreams.a
+desktop: BOOST_LIB_PO=/usr/local/lib/libboost_program_options.a
+desktop: $(BFILE)
+
+olivier: HTSSRC=$(HOME)/Tools
+olivier: HTSLIB_INC=$(HTSSRC)/htslib-1.9
+olivier: HTSLIB_LIB=$(HTSSRC)/htslib-1.9/libhts.a
+olivier: BOOST_INC=/usr/include
+olivier: BOOST_LIB_IO=/usr/lib/x86_64-linux-gnu/libboost_iostreams.a
+olivier: BOOST_LIB_PO=/usr/lib/x86_64-linux-gnu/libboost_program_options.a
+olivier: $(BFILE)
+
+curnagl: DYN_LIBS=-lz -lpthread -lcrypto /dcsrsoft/spack/hetre/v1.1/spack/opt/spack/linux-rhel8-zen2/gcc-9.3.0/xz-5.2.5-3zvzfm67t6ebuerybemshylrysbphghz/lib/liblzma.so /dcsrsoft/spack/hetre/v1.1/spack/opt/spack/linux-rhel8-zen2/gcc-9.3.0/bzip2-1.0.8-tsmb67uwhlqn5g6h6etjvftugq7y6mtl/lib/libbz2.so /dcsrsoft/spack/hetre/v1.1/spack/opt/spack/linux-rhel8-zen2/gcc-9.3.0/curl-7.74.0-fcqjhj645xhqp2ilrzafwqtqqnu7g42v/lib/libcurl.so
+curnagl: HTSSRC=/dcsrsoft/spack/hetre/v1.1/spack/opt/spack/linux-rhel8-zen2/gcc-9.3.0/htslib-1.12-p4n5q4icj4g5e4of7mxq2i5xly4v4tax
+curnagl: HTSLIB_INC=$(HTSSRC)/include
+curnagl: HTSLIB_LIB=$(HTSSRC)/lib/libhts.a
+curnagl: BOOST_INC=/dcsrsoft/spack/hetre/v1.1/spack/opt/spack/linux-rhel8-zen2/gcc-9.3.0/boost-1.74.0-yazg3k7kwtk64o3ljufuoewuhcjqdtqp/include
+curnagl: BOOST_LIB_IO=/dcsrsoft/spack/hetre/v1.1/spack/opt/spack/linux-rhel8-zen2/gcc-9.3.0/boost-1.74.0-yazg3k7kwtk64o3ljufuoewuhcjqdtqp/lib/libboost_iostreams.a
+curnagl: BOOST_LIB_PO=/dcsrsoft/spack/hetre/v1.1/spack/opt/spack/linux-rhel8-zen2/gcc-9.3.0/boost-1.74.0-yazg3k7kwtk64o3ljufuoewuhcjqdtqp/lib/libboost_program_options.a
+curnagl: $(BFILE)
+
+jura: HTSSRC=/scratch/beegfs/FAC/FBM/DBC/odelanea/default_sensitive/data/libs/htslib-1.12
+jura: HTSLIB_INC=$(HTSSRC)
+jura: HTSLIB_LIB=$(HTSSRC)/libhts.a
+jura: BOOST_INC=/scratch/beefgs/FAC/FBM/DBC/odelanea/default_sensitive/data/libs/boost/include
+jura: BOOST_LIB_IO=/scratch/beefgs/FAC/FBM/DBC/odelanea/default_sensitive/data/libs/boost/lib/libboost_iostreams.a
+jura: BOOST_LIB_PO=/scratch/beefgs/FAC/FBM/DBC/odelanea/default_sensitive/data/libs/boost/lib/libboost_program_options.a
+jura: $(BFILE)
+
+wally: HTSSRC=/scratch/wally/FAC/FBM/DBC/odelanea/default/libs/htslib_v1.12
+wally: HTSLIB_INC=$(HTSSRC)
+wally: HTSLIB_LIB=$(HTSSRC)/libhts.a
+wally: BOOST_INC=/scratch/wally/FAC/FBM/DBC/odelanea/default/libs/boost/include
+wally: BOOST_LIB_IO=/scratch/wally/FAC/FBM/DBC/odelanea/default/libs/boost/lib/libboost_iostreams.a
+wally: BOOST_LIB_PO=/scratch/wally/FAC/FBM/DBC/odelanea/default/libs/boost/lib/libboost_program_options.a
+wally: $(BFILE)
+
+static_exe: CXXFLAG=-O2 -D__COMMIT_ID__=\"$(COMMIT_VERS)\" -D__COMMIT_DATE__=\"$(COMMIT_DATE)\"
+static_exe: LDFLAG=-O2
+static_exe: HTSSRC=../..
+static_exe: HTSLIB_INC=$(HTSSRC)/htslib_minimal
+static_exe: HTSLIB_LIB=$(HTSSRC)/htslib_minimal/libhts.a
+static_exe: BOOST_INC=/usr/include
+static_exe: BOOST_LIB_IO=/usr/local/lib/libboost_iostreams.a
+static_exe: BOOST_LIB_PO=/usr/local/lib/libboost_program_options.a
+static_exe: $(EXEFILE)
+
+#COMPILATION RULES
+all: desktop
+
+$(BFILE): $(OFILE)
+	$(CXX) $(LDFLAG) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) -o $@ $(DYN_LIBS)
+
+$(EXEFILE): $(OFILE)
+	$(CXX) $(LDFLAG) -static -static-libgcc -static-libstdc++ -pthread -o $(EXEFILE) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) -Wl,-Bstatic $(DYN_LIBS)
+
+obj/%.o: %.cpp $(HFILE)
+	$(CXX) $(CXXFLAG) -c $< -o $@ -Isrc -I$(HTSLIB_INC) -I$(BOOST_INC)
+
+clean: 
+	rm -f obj/*.o $(BFILE) $(EXEFILE)

convert/src/converter/converter_algorithm.cpp

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+////////////////////////////////////////////////////////////////////////////////
+// Copyright (C) 2018 Olivier Delaneau, University of Lausanne
+// 
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+// 
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+// 
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+////////////////////////////////////////////////////////////////////////////////
+#include <converter/converter_header.h>
+
+#include <io/sparse2plain.h>
+#include <io/plain2sparse.h>
+
+void converter::convert() {
+
+	int mode1 = options.count("input-plain") + options.count("output-sparse");
+	int mode2 = options.count("input-sparse") + options.count("output-plain");
+
+	if (mode1==2 && mode2==0) {
+		plain2sparse(options["input-plain"].as < string > (), options["output-sparse"].as < string > (), options["region"].as < string > (), options["thread"].as < int > (), options["maf"].as < double > ()).convert();
+	} else if (mode1==0 && mode2==2) {
+		sparse2plain(options["output-plain"].as < string > (), options["input-sparse"].as < string > (), options["region"].as < string > (), options["thread"].as < int > ()).convert();
+	}
+
+}

convert/src/converter/converter_finalise.cpp

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+////////////////////////////////////////////////////////////////////////////////
+// Copyright (C) 2018 Olivier Delaneau, University of Lausanne
+// 
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+// 
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+// 
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+////////////////////////////////////////////////////////////////////////////////
+#include <converter/converter_header.h>
+
+void converter::write_files_and_finalise() {
+	vrb.title("Finalization:");
+
+	//step0: Measure overall running time
+	vrb.bullet("Total running time = " + stb.str(tac.abs_time()) + " seconds");
+}

convert/src/converter/converter_header.h

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+/*******************************************************************************
+ * Copyright (C) 2018 Olivier Delaneau, University of Lausanne
+ * 
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ * 
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ * 
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
+
+#ifndef _CONVERTER_H
+#define _CONVERTER_H
+
+#include <utils/otools.h>
+
+class converter {
+public:
+	//COMMAND LINE OPTIONS
+	bpo::options_description descriptions;
+	bpo::variables_map options;
+
+	//CONSTRUCTOR
+	converter();
+	~converter();
+
+	//METHODS
+	void convert();
+
+	//PARAMETERS
+	void declare_options();
+	void parse_command_line(vector < string > &);
+	void check_options();
+	void verbose_options();
+	void verbose_files();
+
+	//
+	void read_files_and_initialise();
+	void convert(vector < string > &);
+	void write_files_and_finalise();
+};
+
+
+#endif
+
+

convert/src/converter/converter_initialise.cpp

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+////////////////////////////////////////////////////////////////////////////////
+// Copyright (C) 2018 Olivier Delaneau, University of Lausanne
+// 
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+// 
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+// 
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+////////////////////////////////////////////////////////////////////////////////
+#include <converter/converter_header.h>
+
+void converter::read_files_and_initialise() {
+
+	//step0: Initialize seed
+	rng.setSeed(options["seed"].as < int > ());
+}

convert/src/converter/converter_management.cpp

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+////////////////////////////////////////////////////////////////////////////////
+// Copyright (C) 2018 Olivier Delaneau, University of Lausanne
+// 
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+// 
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+// 
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+////////////////////////////////////////////////////////////////////////////////
+#include <converter/converter_header.h>
+
+converter::converter() {
+}
+
+converter::~converter() {
+}
+
+void converter::convert(vector < string > & args) {
+	declare_options();
+	parse_command_line(args);
+	check_options();
+	verbose_files();
+	verbose_options();
+	read_files_and_initialise();
+	convert();
+	write_files_and_finalise();
+}