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)
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