ax_lib_samtools
===============

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)

Source Code
***********

Download the latest version of ax_lib_samtools.m4 (http://git.savannah.gnu.org/gitweb/?p=autoconf-archive.git;a=blob_plain;f=m4/ax_lib_samtools.m4) or browse the macro's revision history (http://git.savannah.gnu.org/gitweb/?p=autoconf-archive.git;a=history;f=m4/ax_lib_samtools.m4).

License
*******

Copyright © 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.