/usr/include/jellyfish/parser_common.hpp is in libjellyfish-2.0-dev 2.2.8-3build1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 | /* This file is part of Jellyfish.
Jellyfish 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.
Jellyfish 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 Jellyfish. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef __JELLYFISH_PARSER_COMMON_H__
#define __JELLYFISH_PARSER_COMMON_H__
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <memory>
#include <jellyfish/sam_format.hpp>
namespace jellyfish {
enum file_type { DONE_TYPE
, FASTA_TYPE
, FASTQ_TYPE
#ifdef HAVE_HTSLIB
, SAM_TYPE
#endif
};
struct stream_type {
std::unique_ptr<std::istream> standard;
#ifdef HAVE_HTSLIB
std::unique_ptr<sam_wrapper> sam;
#endif
bool good() {
return (standard && standard->good())
#ifdef HAVE_HTSLIB
|| (sam && sam->good())
#endif
;
}
void reset() {
standard.reset();
#ifdef HAVE_HTSLIB
sam.reset();
#endif
}
};
}
#endif // __JELLYFISH_PARSER_COMMON_H__
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