/usr/include/SeqLib/UnalignedSequence.h is in libseqlib-dev 1.1.1+dfsg-5.
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 | #ifndef SEQLIB_UNALIGNED_SEQ_H__
#define SEQLIB_UNALIGNED_SEQ_H__
extern "C" {
#include "bwa/bwa.h"
#include "bwa/bwt.h"
#include "bwa/bntseq.h"
#include "bwa/kseq.h"
#include <stdlib.h>
#include "bwa/utils.h"
#include "bwa/bwamem.h"
int is_bwt(ubyte_t *T, int n);
KSEQ_DECLARE(gzFile)
}
#include <cstring>
#include <vector>
namespace SeqLib {
/** Structure to hold unaligned sequence (name and bases)
*/
struct UnalignedSequence {
/** Construct an empty sequence */
UnalignedSequence() {}
/** Construct an unaliged sequence with name and sequence
* @param n Name of the sequence
* @param s Sequence, stored as ACTG or N characters
*/
UnalignedSequence(const std::string& n, const std::string& s) : Name(n), Seq(s), Qual(std::string()), Strand('*') {}
/** Construct an unaliged sequence with name, sequence and quality score
* @param n Name of the sequence
* @param s Sequence, stored as ACTG or N characters
* @param q Quality string
*/
UnalignedSequence(const std::string& n, const std::string& s, const std::string& q) : Name(n), Seq(s), Qual(q), Strand('*') {}
/** Construct an unaliged sequence with name, sequence and quality score
* @param n Name of the sequence
* @param s Sequence, stored as ACTG or N characters
* @param q Quality string
* @param t Strand of the sequence, one of '*', '+', '-'
*/
UnalignedSequence(const std::string& n, const std::string& s, const std::string& q, char t) : Name(n), Seq(s), Qual(q), Strand(t) {}
std::string Name; ///< Name of the contig
std::string Seq; ///< Sequence of the contig (upper-case ACTGN)
std::string Qual; ///< Quality scores
char Strand; ///< Strand of the sequence. Default is '*'
};
typedef std::vector<UnalignedSequence> UnalignedSequenceVector; ///< A collection of unaligned sequences
}
#endif
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