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#ifndef ALIGNMENT_H
#define ALIGNMENT_H 1
#include <cassert>
#include <istream>
#include <ostream>
#include <string>
/** An ungapped alignment of a query to a target. */
struct Alignment
{
std::string contig;
int contig_start_pos;
int read_start_pos;
int align_length;
int read_length;
bool isRC;
Alignment() { }
Alignment(const Alignment& o,
std::string /*qid*/, std::string /*seq*/) { *this = o; }
Alignment(std::string contig, int contig_start, int read_start,
int align_length, int read_length, bool isRC) :
contig(contig),
contig_start_pos(contig_start),
read_start_pos(read_start),
align_length(align_length),
read_length(read_length),
isRC(isRC)
{
}
/**
* Return the taret position at the query start.
* Note: not alignment start, and may be negative
*/
int targetAtQueryStart() const
{
unsigned tend = contig_start_pos + align_length;
return !isRC ? contig_start_pos - read_start_pos
: int(tend + read_start_pos);
}
/** Return the distance between the specified alignments.
* May be used to calculate fragment size when the alignments are
* mate pairs.
*/
int operator-(const Alignment& o) const
{
return targetAtQueryStart() - o.targetAtQueryStart();
}
/** Return an alignment of the reverse complement of the query to
* the same target.
*/
Alignment flipQuery() const
{
Alignment rc(*this);
unsigned qend = read_start_pos + align_length;
assert(qend <= (unsigned)read_length);
rc.read_start_pos = read_length - qend;
rc.isRC = !isRC;
return rc;
}
static int calculateReverseReadStart(int read_start_pos,
int read_length, int align_length)
{
unsigned qend = read_start_pos + align_length;
return read_length - qend;
}
bool operator<(const Alignment& a1) const
{
return read_start_pos < a1.read_start_pos;
}
friend std::istream& operator >>(std::istream& in, Alignment& a)
{
return in >> a.contig
>> a.contig_start_pos
>> a.read_start_pos
>> a.align_length
>> a.read_length
>> a.isRC;
}
friend std::ostream& operator <<(std::ostream& out,
const Alignment& a)
{
return out << a.contig << ' '
<< a.contig_start_pos << ' '
<< a.read_start_pos << ' '
<< a.align_length << ' '
<< a.read_length << ' '
<< a.isRC;
}
}; // struct Alignment
#endif
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