void
starling_read::
set_genome_align(const alignment& al) {

    assert(get_full_segment().genome_align().empty());
    assert(! al.empty());

    get_full_segment()._genome_align=al;
    const seg_id_t n_seg(apath_exon_count(al.path));
    if(n_seg<=1) return;

    // deal with segmented reads now:
    assert(! is_segmented());
    _segment_ptr.reset(new starling_segmented_read(n_seg));

    using namespace ALIGNPATH;

    seg_id_t seg_id(1);
    pos_t read_pos(0);
    pos_t ref_pos(al.pos);
    pos_t seg_start_read_pos(read_pos);
    pos_t seg_start_ref_pos(ref_pos);
    path_t seg_path;

    const unsigned as(al.path.size());
    for(unsigned i(0); i<as; ++i) {
        const path_segment& ps(al.path[i]);
        const pos_t last_read_pos(read_pos);
        if(is_segment_type_ref_length(ps.type)) ref_pos += ps.length;
        if(is_segment_type_read_length(ps.type)) read_pos += ps.length;

        if(ps.type!=SKIP) seg_path.push_back(ps);

        if(ps.type==SKIP || ((i+1)==as)) {
            const pos_t end_read_pos( (ps.type==SKIP) ?
                                      last_read_pos : read_pos );
            assert(end_read_pos>seg_start_read_pos);
            const unsigned size(end_read_pos-seg_start_read_pos);
            const read_segment rseg(size,seg_start_read_pos,this);
            _segment_ptr->set_segment(seg_id,rseg);
            alignment& new_al(get_segment(seg_id)._genome_align);
            new_al.path=seg_path;
            new_al.pos=seg_start_ref_pos;
            new_al.is_fwd_strand=al.is_fwd_strand;

            seg_id++;
            seg_start_read_pos=read_pos;
            seg_start_ref_pos=ref_pos;
            seg_path.clear();
        }
    }
}