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AC_INIT([MUMmer],[4.0.1],[[email protected]])

AC_CANONICAL_HOST

AC_CONFIG_MACRO_DIR([m4])

AM_INIT_AUTOMAKE([subdir-objects foreign parallel-tests color-tests])

AM_SILENT_RULES([yes])

AC_CONFIG_SRCDIR([.])

AC_CONFIG_HEADERS([config.h])

LT_INIT

# Check for compiler and flags

AS_IF([test -z "$CXXFLAGS"], [cxxflags_given=no], [cxxflags_given=yes])

AC_LANG(C++)

AC_PROG_CXX

AC_PROG_CC

AC_PATH_PROG(ENV_PROG, [env])

AS_IF([test x$cxxflags_given = xno], [CXXFLAGS="-DNDEBUG $CXXFLAGS"])

EXTRA_CXXFLAGS=

AC_SUBST([EXTRA_CXXFLAGS])

# Check for openmp

AC_ARG_ENABLE([openmp], [AS_HELP_STRING([--disable-openmp], [Disable OpenMP, even if available])])

AS_IF([test "x$enable_openmp" != "xno"],

# OpenMP enabled. Check if available

[AX_OPENMP([AC_DEFINE(HAVE_OPENMP,1,[Define if OpenMP is enabled])])]

[EXTRA_CXXFLAGS="$EXTRA_CXXFLAGS $OPENMP_CXXFLAGS"],

# OpenMP disabled. Ignore pragma warnings

[EXTRA_CXXFLAGS="$EXTRA_CXXFLAGS -Wno-unknown-pragmas"])

# Check for yaggo

AC_ARG_VAR([YAGGO], [Path to the yaggo switch parser generator])

AS_IF([test "x$YAGGO" = "x"], [AC_PATH_PROG([YAGGO], [yaggo], [false])])

# Check for samtools. Only used for testing if available

AC_ARG_VAR([SAMTOOLS], [Path to sammtools (for testing only, optional)])

AS_IF([test "x$SAMTOOLS" = "x"], [AC_PATH_PROG([SAMTOOLS], [samtools])])

# Check that type __int128 is supported and if the

AC_ARG_WITH([int128],

[AS_HELP_STRING([--with-int128], [enable int128])],

[], [with_int128=yes])

AS_IF([test "x$with_int128" != xno],

[AC_CHECK_TYPE([__int128],

[AC_DEFINE([HAVE_INT128], [1], [Define if type __int128 is supported])])])

# Check if std::thread::sleep_for is supported

AC_MSG_CHECKING([if std::thread::sleep_for is supported])

try_nano_sleep=

AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[#include <thread>]],

[[std::this_thread::sleep_for(std::chrono::seconds(1))]])],

[AC_MSG_RESULT([yes])], [try_nano_sleep=yes])

AS_IF([test x$try_nano_sleep = xyes],

[save_cxxflags="$CXXFLAGS"]

[CXXFLAGS="-D_GLIBCXX_USE_NANOSLEEP $CXXFLAGS"]

[AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[#include <thread>]],

[[std::this_thread::sleep_for(std::chrono::seconds(1))]])],

[AC_MSG_RESULT([yes])]

[EXTRA_CXXFLAGS="-D_GLIBCXX_USE_NANOSLEEP $EXTRA_CXXFLAGS"],

[AC_MSG_RESULT([no])]

[AC_MSG_FAILURE([Compiler does not support std::this_thread::sleep_for])])]

[CXXFLAGS="$save_cxxflags"])

# SWIG and bindings

need_shared_libraries=no

# --enable-python-binding

AC_ARG_ENABLE([python-binding],

[AS_HELP_STRING([--enable-python-binding@<:@=PATH@:>@],[create SWIG python module and install in PATH])])

# --enable-ruby-binding

AC_ARG_ENABLE([ruby-binding],

[AS_HELP_STRING([--enable-ruby-binding@<:@=PATH@:>@],[create SWIG ruby module and install in PATH])])

# --enable-perl-binding

AC_ARG_ENABLE([perl-binding],

[AS_HELP_STRING([--enable-perl-binding@<:@=PATH@:>@],[create SWIG perl module and install in PATH])])

# --enable-all-binding

AC_ARG_ENABLE([all-binding],

[AS_HELP_STRING([--enable-all-binding@<:@=PATH@:>@],[create SWIG module for all languages and install in PATH])])

# --enable-swig

AC_ARG_ENABLE([swig],

[AS_HELP_STRING([--enable-swig],[enable development of swig binding])])

AS_IF([test x$enable_swig = xyes],

[AX_PKG_SWIG([3.0.0], [], [AC_MSG_ERROR([SWIG version 3 is required])])])

AS_IF([test -n "$SWIG"],

[AX_SWIG_ENABLE_CXX])

AM_CONDITIONAL([HAVE_SWIG], [test -n "$SWIG"])

# Python binding setup

AS_IF([test -z "$enable_python_binding"], [enable_python_binding="$enable_all_binding"])

AM_CONDITIONAL(PYTHON_BINDING, [test -n "$enable_python_binding" -a x$enable_python_binding != xno])

AM_COND_IF([PYTHON_BINDING],

[AS_IF([test "x$enable_python_binding" != xyes], [PYTHON_SITE_PKG=$enable_python_binding],

[test "x$prefix" != xNONE], [PYTHON_SITE_PKG=$libdir/python])]

[AX_PYTHON_DEVEL]

[need_shared_libraries=yes])

# Ruby binding setup

AS_IF([test -z "$enable_ruby_binding"], [enable_ruby_binding="$enable_all_binding"])

AM_CONDITIONAL([RUBY_BINDING], [test -n "$enable_ruby_binding" -a x$enable_ruby_binding != xno])

AM_COND_IF([RUBY_BINDING],

[AS_IF([test "x$enable_ruby_binding" != xyes], [RUBY_EXT_LIB=$enable_ruby_binding],

[test "x$prefix" != xNONE], [RUBY_EXT_LIB=$libdir/ruby])]

[AX_RUBY_EXT]

[need_shared_libraries=yes])

# Perl binding setup

AS_IF([test -z "$enable_perl_binding"], [enable_perl_binding="$enable_all_binding"])

AM_CONDITIONAL([PERL_BINDING], [test -n "$enable_perl_binding" -a x$enable_perl_binding != xno])

AM_COND_IF([PERL_BINDING],

[AS_IF([test "x$enable_perl_binding" != xyes], [PERL_EXT_LIB=$enable_perl_binding],

[test "x$prefix" != xNONE], [PERL_EXT_LIB=$libdir/perl])]

[need_shared_libraries=yes])

# Look for Perl even if no binding desired. It is required for some

# scripts (e.g. mummerplot)

AX_PERL_EXT

AS_IF([test x"$PERL" = x], [AC_MSG_ERROR([Perl5 not found])])

# Check that shared libraries are enabled if needed by SWIG bindings

AS_IF([test "x$need_shared_libraries" = xyes -a "x$enable_shared" = xno],

[AC_MSG_ERROR([Shared libraries are required for the SWIG script binding but are disabled (probably by the switch --disable-shared)])])

AS_IF([test "x$need_shared_libraries" = xyes -a "x$can_build_shared" = xno],

[AC_MSG_ERROR([Shared libraries (modules) are required for the SWIG script binding but cannot be build (probably not supported by the compiler)])])

AC_MSG_NOTICE([compiling with flags: CXXFLAGS=$CXXFLAGS])

AC_CONFIG_FILES([Makefile mummer.pc])

AC_OUTPUT