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# ===========================================================================
# https://www.gnu.org/software/autoconf-archive/ax_lib_samtools.html
# ===========================================================================
#
# SYNOPSIS
#
# AX_LIB_SAMTOOLS()
#
# DESCRIPTION
#
# This macro searches for an installed samtools library. If nothing was
# specified when calling configure, it searches first in /usr/local and
# then tries with ld's default library search path. If the
# --with-samtools=DIR is specified, it will try to find it in
# DIR/include/bam/sam.h and DIR/lib/libbam.a. As a final try it will look
# in DIR/sam.h and DIR/libbam.a as the samtools library does not contain
# an install rule.
#
# If --without-samtools is specified, the library is not searched at all.
#
# If either the header file (sam.h) or the library (libbam) is not found,
# the configuration exits on error, asking for a valid samtools
# installation directory or --without-samtools.
#
# The macro defines the symbol HAVE_SAMTOOLS if the library is found. You
# should use autoheader to include a definition for this symbol in a
# config.h file. Sample usage in a C/C++ source is as follows:
#
# #ifdef HAVE_SAMTOOLS
# #include <sam.h>
# #endif /* HAVE_SAMTOOLS */
#
# The following output variables are set with AC_SUBST:
#
# SAMTOOLS_CPPFLAGS
# SAMTOOLS_LDFLAGS
# SAMTOOLS_LIBS
#
# You can use them like this in Makefile.am:
#
# AM_CPPFLAGS = $(SAMTOOLS_CPPFLAGS)
# AM_LDFLAGS = $(SAMTOOLS_LDFLAGS)
# program_LDADD = $(SAMTOOLS_LIBS)
#
# LICENSE
#
# Copyright (c) 2013 Timothy Brown <tbrown@freeshell.org>
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
# Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program. If not, see <https://www.gnu.org/licenses/>.
#
# As a special exception, the respective Autoconf Macro's copyright owner
# gives unlimited permission to copy, distribute and modify the configure
# scripts that are the output of Autoconf when processing the Macro. You
# need not follow the terms of the GNU General Public License when using
# or distributing such scripts, even though portions of the text of the
# Macro appear in them. The GNU General Public License (GPL) does govern
# all other use of the material that constitutes the Autoconf Macro.
#
# This special exception to the GPL applies to versions of the Autoconf
# Macro released by the Autoconf Archive. When you make and distribute a
# modified version of the Autoconf Macro, you may extend this special
# exception to the GPL to apply to your modified version as well.
#serial 4
AC_DEFUN([AX_LIB_SAMTOOLS],
#
# Handle user hints
#
[AC_MSG_CHECKING([if samtools is wanted])
AC_ARG_WITH([samtools],
AS_HELP_STRING([--with-samtools],
[search for samtools in DIR/include and DIR/lib]),
[if test "$withval" != no ; then
AC_MSG_RESULT([yes])
if test -d "$withval" ; then
SAMTOOLS_HOME="$withval"
else
AC_MSG_WARN([Sorry, $withval does not exist, checking usual places])
fi
else
AC_MSG_RESULT([no])
fi],
[AC_MSG_RESULT([yes])])
if test -f "${SAMTOOLS_HOME}/include/bam/sam.h" ; then
SAMTOOLS_INCDIR="-I${SAMTOOLS_HOME}/include/bam"
SAMTOOLS_LIBDIR="-L${SAMTOOLS_HOME}/lib"
elif test -f "${SAMTOOLS_HOME}/include/sam.h" ; then
SAMTOOLS_INCDIR="-I${SAMTOOLS_HOME}/include"
SAMTOOLS_LIBDIR="-L${SAMTOOLS_HOME}/lib"
elif test -f "${SAMTOOLS_HOME}/sam.h" ; then
SAMTOOLS_INCDIR="-I${SAMTOOLS_HOME}"
SAMTOOLS_LIBDIR="-L${SAMTOOLS_HOME}"
elif test -f "/usr/local/include/bam/sam.h" ; then
SAMTOOLS_HOME="/usr/local"
SAMTOOLS_INCDIR="-I${SAMTOOLS_HOME}/include/bam"
SAMTOOLS_LIBDIR="-L${SAMTOOLS_HOME}/lib"
else
SAMTOOLS_HOME="/usr"
SAMTOOLS_INCDIR="-I${SAMTOOLS_HOME}/include/bam"
SAMTOOLS_LIBDIR=""
fi
#
# Locate samtools, if wanted
#
if test -n "${SAMTOOLS_HOME}" ; then
SAMTOOLS_OLD_LDFLAGS=$LDFLAGS
SAMTOOLS_OLD_CPPFLAGS=$LDFLAGS
LDFLAGS="$LDFLAGS ${SAMTOOLS_LIBDIR}"
CPPFLAGS="$CPPFLAGS ${SAMTOOLS_INCDIR}"
AC_LANG_PUSH([C])
AC_CHECK_HEADER([sam.h], [ac_cv_sam_h=yes], [ac_cv_sam_h=no])
AC_CHECK_LIB([bam], [sam_open], [ac_cv_libbam=yes], [ac_cv_libbam=no])
AC_LANG_POP([C])
if test "$ac_cv_libbam" = "yes" && test "$ac_cv_sam_h" = "yes" ; then
#
# If both library and header were found, use them
#
AC_MSG_CHECKING([samtools])
AC_MSG_RESULT([ok])
with_samtools=yes
else
#
# If either header or library was not found, revert and bomb
#
LDFLAGS="$SAMTOOLS_OLD_LDFLAGS"
CPPFLAGS="$SAMTOOLS_OLD_CPPFLAGS"
AC_MSG_CHECKING([samtools])
AC_MSG_RESULT([failed])
AC_MSG_ERROR([either specify a valid samtools installation with --with-samtools=DIR or disable samtools usage with --without-samtools])
fi
fi
])
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