Initial commit of VCFtools project

Makefile

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+#
+# 1) Compiling
+#   Type make in this directory
+#
+# 2) Installation
+#   Edit the BINDIR and MODDIR below as necessary or pass the PREFIX variable
+#   to the make command. When not set, the programs will be placed in "bin" 
+#   and "lib" subdirectories in this directory.
+#       PREFIX="/install/to/path/prefix" make install
+#
+#   Add the MODDIR to your PERL5LIB environment variable:
+#       export PERL5LIB=${PREFIX}/lib:${PERL5LIB}
+#
+#   Add the MANDIR to your MANPATH environment variable:
+#       export MANPATH=${PREFIX}/bin:$MANPATH
+#
+
+export SRCDIR = $(dir $(realpath $(lastword $(MAKEFILE_LIST))))
+ifndef PREFIX
+    export PREFIX = ${SRCDIR}
+endif
+export BINDIR = ${PREFIX}/bin
+export MANDIR = ${PREFIX}/bin/man1
+export MODDIR = ${PREFIX}/lib/perl5/site_perl
+
+DIRS = cpp perl
+install:
+	    @mkdir -p $(BINDIR); mkdir -p $(MODDIR); mkdir -p $(MANDIR); \
+	    cp ${SRCDIR}/cpp/vcftools.1 $(MANDIR); \
+        for dir in $(DIRS); do cd $$dir && $(MAKE) $(MAKEFLAGS) && cd ..; done
+
+clean:
+		@for dir in $(DIRS); do cd $$dir && $(MAKE) clean && cd ..; done

README.txt

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+License:
+    The program package is released under the GNU Lesser General Public 
+    License version 3.0 (LGPLv3).
+
+Credits:
+    Adam Auton        (cpp executable)
+    Petr Danecek      (perl)
+    Anthony Marcketta (cpp executable)
+
+Compiling:
+    To compile and install VCFtools, you should type 'make' in the 
+    vcftools folder. The perl scripts and cpp executable will be 
+    installed in the /vcftools_(version_num)/bin/ folder. It is 
+    recommended that you add this folder to you PATH.
+
+Documentation:
+    The latest version of the documentation and examples of usage can be 
+    found in the website subdirectory or go online:
+         http://vcftools.sourceforge.net/docs.html
+
+Getting Help:
+    The best way to get help regarding VCFtools is to email the mailing
+    list: vcftools-help@lists.sourceforge.net 
+
+Citation:
+    If you make use of VCFtools in your research, we would appreciate a 
+    citation of the following paper:
+
+    The Variant Call Format and VCFtools, 
+    Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, 
+    Eric Banks, Mark A. DePristo, Robert Handsaker, Gerton Lunter, 
+    Gabor Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin 
+    and 1000 Genomes Project Analysis Group, Bioinformatics, 2011
+
+    http://dx.doi.org/10.1093/bioinformatics/btr330
+
+

cpp/Makefile

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+# Make file for vcftools
+# Author: Adam Auton
+# ($Revision: 230 $)
+
+# Compiler
+CC = gcc
+CPP = g++
+# Output executable
+EXECUTABLE = vcftools
+# Flag used to turn on compilation of PCA routines
+ifndef VCFTOOLS_PCA
+	VCFTOOLS_PCA = 0
+endif
+# Compiler flags
+CFLAGS = -O2 -m64
+#CFLAGS = -Wall -O2 -pg -m64
+CPPFLAGS = -O2 -D_FILE_OFFSET_BITS=64 
+#CPPFLAGS = -O2 -Wall -pg -D_FILE_OFFSET_BITS=64
+# Included libraries (zlib)
+LIB = -lz 
+#LIB = -lz -I/opt/local/include/ -L/opt/local/lib/
+
+OBJS = vcftools.o bcf_file.o vcf_file.o variant_file.o \
+	header.o bcf_entry.o vcf_entry.o entry.o entry_getters.o entry_setters.o \
+	vcf_entry_setters.o bcf_entry_setters.o entry_filters.o variant_file_filters.o variant_file_output.o parameters.o \
+	variant_file_format_convert.o variant_file_diff.o output_log.o bgzf.o gamma.o
+
+ifeq ($(VCFTOOLS_PCA), 1)
+	# Define flag for PCA routine compilation
+	CPPFLAGS += -DVCFTOOLS_PCA
+	# Add LAPACK library
+	LIB += -llapack	
+	# Add PCA source code
+	OBJS+= dgeev.o
+endif
+
+vcftools: $(OBJS)
+	$(CPP) $(CPPFLAGS) $(OBJS) -o vcftools $(LIB)
+ifdef BINDIR
+	cp $(CURDIR)/$@ $(BINDIR)/$@
+endif
+
+bgzf: bgzf.c
+	$(CC) -c $(CFLAGS) $(FLAGS) bgzf.c $(LIB) -o bgzf.o
+
+# pull in dependency info for *existing* .o files
+-include $(OBJS:.o=.d)
+
+%.o: %.cpp
+	$(CPP) -c $(CPPFLAGS) $*.cpp -o $*.o
+	$(CPP) -MM $(CPPFLAGS) $*.cpp > $*.d
+
+# remove compilation products
+clean:
+	@rm -f vcftools *.o *.d
+	@rm -f $(BINDIR)/vcftools

cpp/Makefile~

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+# Make file for vcftools
+# Author: Adam Auton
+# ($Revision: 230 $)
+
+# Compiler
+CC = gcc
+CPP = g++
+# Output executable
+EXECUTABLE = vcftools
+# Flag used to turn on compilation of PCA routines
+ifndef VCFTOOLS_PCA
+	VCFTOOLS_PCA = 0
+endif
+# Compiler flags
+CFLAGS = -O2 -m64
+#CFLAGS = -Wall -O2 -pg -m64
+CPPFLAGS = -static-libgcc -O2 -D_FILE_OFFSET_BITS=64 
+#CPPFLAGS = -O2 -Wall -pg -D_FILE_OFFSET_BITS=64
+# Included libraries (zlib)
+LIB = -lz 
+#LIB = -lz -I/opt/local/include/ -L/opt/local/lib/
+
+OBJS = vcftools.o bcf_file.o vcf_file.o variant_file.o \
+	header.o bcf_entry.o vcf_entry.o entry.o entry_getters.o entry_setters.o \
+	vcf_entry_setters.o bcf_entry_setters.o entry_filters.o variant_file_filters.o variant_file_output.o parameters.o \
+	variant_file_format_convert.o variant_file_diff.o output_log.o bgzf.o gamma.o
+
+ifeq ($(VCFTOOLS_PCA), 1)
+	# Define flag for PCA routine compilation
+	CPPFLAGS += -DVCFTOOLS_PCA
+	# Add LAPACK library
+	LIB += -llapack	
+	# Add PCA source code
+	OBJS+= dgeev.o
+endif
+
+vcftools: $(OBJS)
+	$(CPP) $(CPPFLAGS) $(OBJS) -o vcftools $(LIB)
+ifdef BINDIR
+	cp $(CURDIR)/$@ $(BINDIR)/$@
+endif
+
+bgzf: bgzf.c
+	$(CC) -c $(CFLAGS) $(FLAGS) bgzf.c $(LIB) -o bgzf.o
+
+# pull in dependency info for *existing* .o files
+-include $(OBJS:.o=.d)
+
+%.o: %.cpp
+	$(CPP) -c $(CPPFLAGS) $*.cpp -o $*.o
+	$(CPP) -MM $(CPPFLAGS) $*.cpp > $*.d
+
+# remove compilation products
+clean:
+	@rm -f vcftools *.o *.d
+	@rm -f $(BINDIR)/vcftools