yat  0.14.5pre
config_bam.h
1 #ifndef theplu_yat_omic_config_bam
2 #define theplu_yat_omic_config_bam
3 
4 // $Id: config_bam.h 3550 2017-01-03 05:41:02Z peter $
5 //
6 // Copyright (C) 2012, 2013, 2014, 2015, 2016 Peter Johansson
7 //
8 // This program is free software; you can redistribute it and/or modify
9 // it under the terms of the GNU General Public License as published by
10 // the Free Software Foundation; either version 3 of the License, or
11 // (at your option) any later version.
12 //
13 // This program is distributed in the hope that it will be useful, but
14 // WITHOUT ANY WARRANTY; without even the implied warranty of
15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
16 // General Public License for more details.
17 //
18 // You should have received a copy of the GNU General Public License
19 // along with this program. If not, see <http://www.gnu.org/licenses/>.
20 
21 /*
22  The purpose of this file is to cater for different installation
23  styles. As samtools' Makefile contains no install rule, different
24  distributions have come up with different ideas where to put
25  samtools' header files. Red Hat put them in '/usr/include/bam'
26  whereas Ubuntu put them in '/usr/include/samtools/'. We could solve
27  this by #including <bam.h> and then add appropriate include path
28  (-I) flags to the compiler, but in order to support arbitrary
29  PREFIX we instead choose to #define macros BAM_HEADER and
30  SAM_HEADER depending on where we found the bam headers (at
31  configure time) as <bam.h>, <bam/bam.h>, or <samtools/bam.h>.
32  */
33 
35 
36 #if defined YAT_HAVE_HTSLIB_HTS_H
37 # define YAT_SAM_HEADER "htslib/sam.h"
38 # define YAT_FAIDX_HEADER "htslib/faidx.h"
39 #elif defined YAT_HAVE_BAM_H
40 # define YAT_BAM_HEADER "bam.h"
41 # define YAT_FAIDX_HEADER "faidx.h"
42 # define YAT_SAM_HEADER "sam.h"
43 #elif defined YAT_HAVE_BAM_BAM_H
44 # define YAT_BAM_HEADER "bam/bam.h"
45 # define YAT_FAIDX_HEADER "bam/faidx.h"
46 # define YAT_SAM_HEADER "bam/sam.h"
47 #elif defined YAT_HAVE_SAMTOOLS_BAM_H
48 # define YAT_BAM_HEADER "samtools/bam.h"
49 # define YAT_FAIDX_HEADER "samtools/faidx.h"
50 # define YAT_SAM_HEADER "samtools/sam.h"
51 #endif
52 
53 #ifndef YAT_SAM_HEADER
54 #error This file requires samtools header files and cannot be used when \
55 yat was configured with switch '--without-htslib'.
56 #endif
57 
58 #endif

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