[BUG] Mixed up output string.

[Irallia]

This bug came out of an discussion of: #49 (comment)

eldariont:
test/api/junction_detection_test.cpp lines +17 to +20:

// Reference\tm2257/8161/CCS\t41972616\tForward\tRead \t0\t2294\tForward\tchr21
// INS from Primary Read - Sequence Type: Reference; Sequence Name: m2257/8161/CCS; Position: 41972616; Orientation: Reverse
//                         Sequence Type: Read; Sequence Name: 0; Position: 3975; Orientation: Reverse
//                         Chromosome: chr21

I'm confused by this string:
// Reference\tm2257/8161/CCS\t41972616\tForward\tRead \t0\t2294\tForward\tchr21
It should consist of breakend1, breakend2 and the read name it was detected from. However, the read name here is chr21 and the reference chromosome of breakend1 is m2257/8161/CCS\t41972616. Those are swapped but I don't immediately see why 😕

---

These output is coming from:
iGenVar/src/detect_breakends/junction_detection.cpp
and are built in:
iGenVar/include/junction.hpp lines 41 to 46:

template <typename stream_t>
inline stream_t operator<<(stream_t && stream, junction const & junc)
{
    stream << junc.get_mate1() << '\t' << junc.get_mate2() << '\t' << junc.get_read_name();
    return stream;
}

iGenVar/include/breakend.hpp lines 35 to 43:

template <typename stream_t>
inline stream_t operator<<(stream_t && stream, breakend const & b)
{
    stream << ((b.seq_type == sequence_type::reference) ? "Reference" : "Read ") << '\t'
           << b.seq_name << '\t'
           << b.position  << '\t'
           << ((b.orientation == strand::forward) ? "Forward" : "Reverse");
    return stream;
}

Probably there is a mixup in the passing of chromosome and read in `retrieve_aligned_segments` or `analyze_cigar`.

[Irallia]

I found the problem. I made a mix up, when I changed the order of the analyze_cigar() parameters. I can open a PR for it.