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#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>
#include <iostream>
namespace SeqLib {
/** Structure to hold unaligned sequence (name and bases)
*/
struct UnalignedSequence {
/** Construct an empty sequence */
UnalignedSequence() {}
/** Construct an unaligned 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), Com(std::string()), Seq(s), Qual(std::string()), Strand('*') {}
/** Construct an unaligned 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), Com(std::string()), Seq(s), Qual(q), Strand('*') {}
/** Construct an unaligned sequence with name, sequence, quality score and strand
* @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), Com(std::string()), Seq(s), Qual(q), Strand(t) {}
std::string Name; ///< Name of the contig
std::string Com; ///< Comment 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 '*'
/** Output an unaligned sequence to ostream
* @param os ostream
* @param us UnalignedSequence
*/
friend std::ostream& operator<<(std::ostream& os, const SeqLib::UnalignedSequence& us){
os << "@" << us.Name << " " << us.Com << "\n";
os << us.Seq << "\n+\n";
os << us.Qual << "\n";
return os;
}
};
typedef std::vector<UnalignedSequence> UnalignedSequenceVector; ///< A collection of unaligned sequences
}
#endif
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