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ax_bam.m4
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ax_bam.m4
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# SYNOPSIS
#
# AX_BAM
#
# DESCRIPTION
#
# Test for the BAM libraries of a particular version (or newer)
#
# If no path to the installed bam library is given the macro searchs
# under /usr, /usr/local, /opt and /opt/local and evaluates the
# $BAM_ROOT environment variable.
# Adapted from AX_BOOST_BASE
#
# This macro calls:
#
# AC_SUBST(BAM_CPPFLAGS) / AC_SUBST(BAM_LDFLAGS)
#
# And sets:
#
# HAVE_BAM
#
# LICENSE
#
# Copyright (c) 2010 Cole Trapnell <[email protected]>
#
# Copying and distribution of this file, with or without modification, are
# permitted in any medium without royalty provided the copyright notice
# and this notice are preserved.
AC_DEFUN([AX_BAM],
[
AC_ARG_WITH([bam],
AS_HELP_STRING([--with-bam@<:@=DIR@:>@], [use BAM libraries (default is yes) - it is possible to specify the root directory for BAM (optional)]),
[
if test "$withval" = "no"; then
want_bam="no"
elif test "$withval" = "yes"; then
want_bam="yes"
ac_bam_path=""
else
want_bam="yes"
ac_bam_path="$withval"
fi
],
[want_bam="yes"])
AC_ARG_WITH([bam-libdir],
AS_HELP_STRING([--with-bam-libdir=LIB_DIR],
[Force given directory for bam libraries. Note that this will overwrite library path detection, so use this parameter only if default library detection fails and you know exactly where your bam libraries are located.]),
[
if test -d $withval
then
ac_bam_lib_path="$withval"
else
AC_MSG_ERROR(--with-bam-libdir expected directory name)
fi
],
[ac_bam_lib_path=""]
)
if test "x$want_bam" = "xyes"; then
# bam_lib_version_req=ifelse([$1], ,1.20.0,$1)
# bam_lib_version_req_shorten=`expr $bam_lib_version_req : '\([[0-9]]*\.[[0-9]]*\)'`
# bam_lib_version_req_major=`expr $bam_lib_version_req : '\([[0-9]]*\)'`
# bam_lib_version_req_minor=`expr $bam_lib_version_req : '[[0-9]]*\.\([[0-9]]*\)'`
# bam_lib_version_req_sub_minor=`expr $bam_lib_version_req : '[[0-9]]*\.[[0-9]]*\.\([[0-9]]*\)'`
# if test "x$bam_lib_version_req_sub_minor" = "x" ; then
# bam_lib_version_req_sub_minor="0"
# fi
# WANT_BAM_VERSION=`expr $bam_lib_version_req_major \* 100000 \+ $bam_lib_version_req_minor \* 100 \+ $bam_lib_version_req_sub_minor`
AC_MSG_CHECKING(for bamlib)
succeeded=no
dnl first we check the system location for bam libraries
if test "$ac_bam_path" != ""; then
BAM_LDFLAGS="-L$ac_bam_path/lib"
BAM_CPPFLAGS="-I$ac_bam_path/include"
else
for ac_bam_path_tmp in /usr /usr/local /opt /opt/local ; do
if test -d "$ac_bam_path_tmp/include/bam" && test -r "$ac_bam_path_tmp/include/bam"; then
BAM_LDFLAGS="-L$ac_bam_path_tmp/lib"
BAM_CPPFLAGS="-I$ac_bam_path_tmp/include"
break;
fi
done
fi
dnl overwrite ld flags if we have required special directory with
dnl --with-bam-libdir parameter
if test "$ac_bam_lib_path" != ""; then
BAM_LDFLAGS="-L$ac_bam_lib_path"
fi
CPPFLAGS_SAVED="$CPPFLAGS"
CPPFLAGS="$CPPFLAGS $BAM_CPPFLAGS"
export CPPFLAGS
LDFLAGS_SAVED="$LDFLAGS"
LDFLAGS="$LDFLAGS $BAM_LDFLAGS"
export LDFLAGS
AC_LANG_PUSH(C++)
AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
@%:@include <bam/bam.h>
]], [[
]])],[
AC_MSG_RESULT(yes)
succeeded=yes
found_system=yes
],[
])
AC_LANG_POP([C++])
dnl if we found no bam with system layout we search for bam libraries
dnl built and installed without the --layout=system option or for a staged(not installed) version
if test "x$succeeded" != "xyes"; then
_version=0
if test "$ac_bam_path" != ""; then
if test -d "$ac_bam_path" && test -r "$ac_bam_path"; then
for i in `ls -d $ac_bam_path/include/bam-* 2>/dev/null`; do
_version_tmp=`echo $i | sed "s#$ac_bam_path##" | sed 's/\/include\/bam-//' | sed 's/_/./'`
V_CHECK=`expr $_version_tmp \> $_version`
if test "$V_CHECK" = "1" ; then
_version=$_version_tmp
fi
VERSION_UNDERSCORE=`echo $_version | sed 's/\./_/'`
BAM_CPPFLAGS="-I$ac_bam_path/include/bam-$VERSION_UNDERSCORE"
done
fi
else
for ac_bam_path in /usr /usr/local /opt /opt/local ; do
if test -d "$ac_bam_path" && test -r "$ac_bam_path"; then
for i in `ls -d $ac_bam_path/include/bam-* 2>/dev/null`; do
_version_tmp=`echo $i | sed "s#$ac_bam_path##" | sed 's/\/include\/bam-//' | sed 's/_/./'`
V_CHECK=`expr $_version_tmp \> $_version`
if test "$V_CHECK" = "1" ; then
_version=$_version_tmp
best_path=$ac_bam_path
fi
done
fi
done
VERSION_UNDERSCORE=`echo $_version | sed 's/\./_/'`
BAM_CPPFLAGS="-I$best_path/include/bam-$VERSION_UNDERSCORE"
if test "$ac_bam_lib_path" = ""
then
BAM_LDFLAGS="-L$best_path/lib"
fi
if test "x$BAM_ROOT" != "x"; then
if test -d "$BAM_ROOT" && test -r "$BAM_ROOT" && test -d "$BAM_ROOT/stage/lib" && test -r "$BAM_ROOT/stage/lib"; then
version_dir=`expr //$BAM_ROOT : '.*/\(.*\)'`
stage_version=`echo $version_dir | sed 's/bam_//' | sed 's/_/./g'`
stage_version_shorten=`expr $stage_version : '\([[0-9]]*\.[[0-9]]*\)'`
V_CHECK=`expr $stage_version_shorten \>\= $_version`
if test "$V_CHECK" = "1" -a "$ac_bam_lib_path" = "" ; then
AC_MSG_NOTICE(We will use a staged bam library from $BAM_ROOT)
BAM_CPPFLAGS="-I$BAM_ROOT"
BAM_LDFLAGS="-L$BAM_ROOT/stage/lib"
fi
fi
fi
fi
CPPFLAGS="$CPPFLAGS $BAM_CPPFLAGS"
export CPPFLAGS
LDFLAGS="$LDFLAGS $BAM_LDFLAGS"
export LDFLAGS
AC_LANG_PUSH(C++)
AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
@%:@include <bam/version.hpp>
]], [[
]])],[
AC_MSG_RESULT(yes)
succeeded=yes
found_system=yes
],[
])
AC_LANG_POP([C++])
fi
if test "$succeeded" != "yes" ; then
if test "$_version" = "0" ; then
AC_MSG_ERROR([[We could not detect the bam libraries (version $bam_lib_version_req_shorten or higher). If you have a staged bam library (still not installed) please specify \$BAM_ROOT in your environment and do not give a PATH to --with-bam option. If you are sure you have bam installed, then check your version number looking in <bam/version.hpp>. See http://randspringer.de/bam for more documentation.]])
else
AC_MSG_NOTICE([Your bam libraries seem too old (version $_version).])
fi
else
BAM_LIB="-lbam"
AC_SUBST(BAM_CPPFLAGS)
AC_SUBST(BAM_LDFLAGS)
AC_SUBST(BAM_LIB)
AC_DEFINE(HAVE_BAM,,[define if the BAM library is available])
fi
CPPFLAGS="$CPPFLAGS_SAVED"
LDFLAGS="$LDFLAGS_SAVED"
fi
])