config_bam.h

#ifndef theplu_yat_omic_config_bam
#define theplu_yat_omic_config_bam

// $Id: config_bam.h 3550 2017-01-03 05:41:02Z peter $
//
// Copyright (C) 2012, 2013, 2014, 2015, 2016 Peter Johansson
//
// 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 <http://www.gnu.org/licenses/>.

/*
   The purpose of this file is to cater for different installation
   styles. As samtools' Makefile contains no install rule, different
   distributions have come up with different ideas where to put
   samtools' header files. Red Hat put them in '/usr/include/bam'
   whereas Ubuntu put them in '/usr/include/samtools/'. We could solve
   this by #including <bam.h> and then add appropriate include path
   (-I) flags to the compiler, but in order to support arbitrary
   PREFIX we instead choose to #define macros BAM_HEADER and
   SAM_HEADER depending on where we found the bam headers (at
   configure time) as <bam.h>, <bam/bam.h>, or <samtools/bam.h>.
 */

#include "yat/utility/config_public.h"

#if defined YAT_HAVE_HTSLIB_HTS_H
#  define YAT_SAM_HEADER "htslib/sam.h"
#  define YAT_FAIDX_HEADER "htslib/faidx.h"
#elif defined YAT_HAVE_BAM_H
#  define YAT_BAM_HEADER "bam.h"
#  define YAT_FAIDX_HEADER "faidx.h"
#  define YAT_SAM_HEADER "sam.h"
#elif defined YAT_HAVE_BAM_BAM_H
#  define YAT_BAM_HEADER "bam/bam.h"
#  define YAT_FAIDX_HEADER "bam/faidx.h"
#  define YAT_SAM_HEADER "bam/sam.h"
#elif defined YAT_HAVE_SAMTOOLS_BAM_H
#  define YAT_BAM_HEADER "samtools/bam.h"
#  define YAT_FAIDX_HEADER "samtools/faidx.h"
#  define YAT_SAM_HEADER "samtools/sam.h"
#endif

#ifndef YAT_SAM_HEADER
#error This file requires samtools header files and cannot be used when \
yat was configured with switch '--without-htslib'.
#endif

#endif