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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:

  #include <sam.h>
  #endif /* HAVE_SAMTOOLS */

The following output variables are set with AC_SUBST:


You can use them like this in

  program_LDADD = $(SAMTOOLS_LIBS)

Source Code

Download the latest version of ax_lib_samtools.m4 or browse the macro’s revision history.


Copyright © 2013 Timothy Brown

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.

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You should have received a copy of the GNU General Public License along with this program. If not, see <>.

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