void short_read_copy(short_read_t* dest, const short_read_t* src)
{
str_copy(&dest->id, &src->id);
str_copy(&dest->seq, &src->seq);
str_copy(&dest->qual, &src->qual);
str_copy(&dest->seqname, &src->seqname);
str_copy(&dest->mate_seqname, &src->mate_seqname);
samopt_table_copy(dest->aux, src->aux);
cigar_copy(&dest->cigar, &src->cigar);
dest->flags = src->flags;
dest->strand = src->strand;
dest->pos = src->pos;
dest->map_qual = src->map_qual;
dest->mate_pos = src->mate_pos;
dest->tlen = src->tlen;
}
void update_seed_left(alig_out_t *alig_out, seed_t *seed, seed_cal_t *cal) {
if (alig_out->match > 0) {
// update seed
seed->num_mismatches += alig_out->mismatch;
seed->num_open_gaps += alig_out->gap_open;
seed->num_extend_gaps += alig_out->gap_extend;
seed->read_start -= alig_out->map_len1;
seed->genome_start -= alig_out->map_len2;
// update cigar with the sw output
if (alig_out->cigar.num_ops > 0) {
cigar_t cigar;
cigar_init(&cigar);
cigar_concat(&seed->cigar, &alig_out->cigar);
cigar_init(&seed->cigar);
cigar_copy(&seed->cigar, &alig_out->cigar);
}
}
}
