/usr/include/jellyfish/sam_format.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 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 | /* 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 __JELYFISH_SAM_FORMAT_H__
#define __JELYFISH_SAM_FORMAT_H__
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#ifdef HAVE_HTSLIB
#include <htslib/sam.h>
namespace jellyfish {
// Manage a sam_stream
class sam_wrapper {
protected:
htsFile* m_fd;
bam_hdr_t* m_header;
bam1_t* m_record;
uint8_t* m_seq;
uint8_t* m_qual;
bool m_eof;
public:
sam_wrapper()
: m_fd(nullptr)
, m_header(nullptr)
, m_record(nullptr)
, m_eof(false)
{ }
sam_wrapper(const char* path)
: m_fd(sam_open(path, "r"))
, m_header(m_fd ? sam_hdr_read(m_fd) : nullptr)
, m_record(m_header ? bam_init1() : nullptr)
, m_eof()
{ }
bool fail() const {
return !m_fd || !m_header || !m_record;
}
// True if stream is good
bool good() const {
return !fail() && !m_eof;
}
operator bool() const { return !fail(); }
// Read next record. Return >= 0 if successful. <0 otherwise.
int next() {
const auto res = sam_read1(m_fd, m_header, m_record);
if(res >= 0) {
m_seq = bam_get_seq(m_record);
m_qual = bam_get_qual(m_record);
} else {
m_eof = true;
}
return res;
}
// Query the content of the record. Valid only after a successful
// next()
const bam1_t* record() { return m_record; }
ssize_t seq_len() const { return m_record->core.l_qseq; }
inline static char decode(int x) {
switch(x) {
case 1: return 'A';
case 2: return 'C';
case 4: return 'G';
case 8: return 'T';
default: return 'N';
}
}
char base(ssize_t i) const { return decode(bam_seqi(m_seq, i)); }
char qual(ssize_t i) const { return m_qual[i]; }
char* qname_str() const { return bam_get_qname(m_record); }
size_t qname_length() const { return m_record->core.l_qname; }
std::string qname() const { return std::string(qname_str(), qname_length()); }
virtual ~sam_wrapper() {
if(m_record) bam_destroy1(m_record);
if(m_header) bam_hdr_destroy(m_header);
if(m_fd) sam_close(m_fd);
}
};
} // jellyfish
#endif // HAVE_HTSLIB
#endif // __JELYFISH_SAM_FORMAT_H__
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