autotools based build

.gitignore

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+# created by autoscan
+
+/autom4te.cache
+/autoscan.log
+/configure.scan
+
+# created by autoreconf -fi (includes autoconf, automake, libtool)
+
+Makefile.in
+/aclocal.m4
+/autom4te.cache
+/compile
+/config.guess
+/config.h.in*
+/config.sub
+/configure
+/depcomp
+/install-sh
+/ltmain.sh
+/m4
+/missing
+
+# created by configure
+
+Makefile
+/config.h
+/config.log
+/config.status
+/libtool
+/stamp-h1
+.deps
+
+# created by make
+
+*.la
+*.lo
+*.o
+.libs
+vcftools
+*.tar.*

Makefile.am

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+ACLOCAL_AMFLAGS = -I m4
+
+SUBDIRS = src

autogen.sh

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+#!/bin/sh
+
+mkdir -p m4
+autoreconf -fi

configure.ac

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+#                                               -*- Autoconf -*-
+# Process this file with autoconf to produce a configure script.
+
+AC_PREREQ([2.69])
+AC_INIT([vcftools], [0.1.13], [https://github.com/vcftools/vcftools/issues])
+AC_CONFIG_MACRO_DIRS([m4])
+AC_CONFIG_SRCDIR([src/cpp/vcftools.cpp])
+AC_CONFIG_HEADERS([config.h])
+
+# Automake invocation.
+AM_INIT_AUTOMAKE([foreign])
+
+# Checks for programs.
+AC_PROG_CXX
+AC_PROG_CC
+AC_PROG_CPP
+
+# Checks for perl.
+AC_PATH_PROGS([PERL], [perl] [perl5], [false])
+if test "x$PERL" = xfalse ; then
+  AC_MSG_ERROR([Perl not found; check your \$PATH.])
+fi
+
+pmdir_relative_path=`\
+$PERL -MConfig \
+      -wle '($_ = $Config{installsitelib})
+            =~ s!^\Q$Config{siteprefix}/!!; \
+            print'`
+
+AC_ARG_WITH(
+    [pmdir],
+    AS_HELP_STRING(
+      [--with-pmdir=DIR],
+      [install Perl modules in DIR]),
+    [PMDIR=${withval}],
+    [PMDIR='${prefix}'/"$pmdir_relative_path"])
+
+AC_SUBST([PMDIR])
+
+# Checks for libraries.
+PKG_CHECK_MODULES(ZLIB, zlib)
+
+# Checks for header files.
+AC_CHECK_HEADERS([arpa/inet.h fcntl.h limits.h netdb.h stdint.h stdlib.h string.h sys/socket.h unistd.h])
+
+# Checks for typedefs, structures, and compiler characteristics.
+AC_CHECK_HEADER_STDBOOL
+AC_C_INLINE
+AC_TYPE_INT16_T
+AC_TYPE_INT32_T
+AC_TYPE_INT64_T
+AC_TYPE_INT8_T
+AC_TYPE_OFF_T
+AC_TYPE_SIZE_T
+AC_TYPE_SSIZE_T
+AC_TYPE_UINT16_T
+AC_TYPE_UINT32_T
+AC_TYPE_UINT8_T
+
+# Checks for library functions.
+AC_FUNC_ERROR_AT_LINE
+AC_FUNC_FSEEKO
+AC_FUNC_MALLOC
+AC_FUNC_REALLOC
+AC_CHECK_FUNCS([gethostbyaddr gethostbyname memset pow select socket sqrt strchr strdup strerror strstr strtol])
+
+AC_CONFIG_FILES([Makefile
+                 src/Makefile
+                 src/cpp/Makefile
+                 src/perl/Makefile])
+AC_OUTPUT

src/Makefile.am

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+SUBDIRS = cpp perl

src/cpp/Makefile.am

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+AM_CFLAGS = -D_FILE_OFFSET_BITS=64
+AM_CXXFLAGS = -D_FILE_OFFSET_BITS=64
+
+bin_PROGRAMS = vcftools
+
+vcftools_CPPFLAGS = $(ZLIB_CPPFLAGS)
+vcftools_LDADD = $(ZLIB_LIBS)
+
+vcftools_SOURCES = \
+	bcf_entry.cpp \
+	bcf_entry.h \
+	bcf_entry_setters.cpp \
+	bcf_file.cpp \
+	bcf_file.h \
+	bgzf.c \
+	bgzf.h \
+	entry.cpp \
+	entry_filters.cpp \
+	entry_getters.cpp \
+	entry.h \
+	entry_setters.cpp \
+	gamma.cpp \
+	gamma.h \
+	header.cpp \
+	header.h \
+	khash.h \
+	knetfile.c \
+	knetfile.h \
+	output_log.cpp \
+	output_log.h \
+	parameters.cpp \
+	parameters.h \
+	variant_file.cpp \
+	variant_file_diff.cpp \
+	variant_file_filters.cpp \
+	variant_file_format_convert.cpp \
+	variant_file.h \
+	variant_file_output.cpp \
+	vcf_entry.cpp \
+	vcf_entry.h \
+	vcf_entry_setters.cpp \
+	vcf_file.cpp \
+	vcf_file.h \
+	vcftools.cpp \
+	vcftools.h
+
+dist_man_MANS = vcftools.1

src/perl/Makefile.am

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+dist_bin_SCRIPTS = \
+	fill-aa \
+	fill-an-ac \
+	fill-fs \
+	fill-ref-md5 \
+	vcf-annotate \
+	vcf-compare \
+	vcf-concat \
+	vcf-consensus \
+	vcf-contrast \
+	vcf-convert \
+	vcf-fix-newlines \
+	vcf-fix-ploidy \
+	vcf-indel-stats \
+	vcf-isec \
+	vcf-merge \
+	vcf-phased-join \
+	vcf-query \
+	vcf-shuffle-cols \
+	vcf-sort \
+	vcf-stats \
+	vcf-subset \
+	vcf-to-tab \
+	vcf-tstv \
+	vcf-validator
+
+pmdir = $(PMDIR)
+
+dist_pm_DATA = \
+	FaSlice.pm \
+	Vcf.pm \
+	VcfStats.pm