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);
}
}
}
void short_read_init(short_read_t* sr)
{
str_init(&sr->id);
str_init(&sr->seq);
str_init(&sr->qual);
str_init(&sr->seqname);
str_init(&sr->mate_seqname);
sr->aux = samopt_table_alloc();
cigar_init(&sr->cigar);
sr->flags = BAM_FUNMAP;
sr->strand = 0;
sr->pos = 0;
sr->map_qual = 255;
sr->mate_pos = 0;
sr->tlen = 0;
}
void extend_to_left(seed_t *seed, int max_length,
seed_cal_t *cal, sa_index3_t *sa_index,
alig_out_t *alig_out) {
cigar_init(&alig_out->cigar);
int chrom = cal->chromosome_id;
//size_t r_end = seed->read_start - 1;
//size_t r_start = r_end - max_length;
size_t r_len = max_length;
char *r_seq = (cal->strand ? cal->read->revcomp : cal->read->sequence);
size_t g_len = r_len + 10;
size_t g_end = seed->genome_start - 1;
size_t g_start = g_end - g_len;
char *g_seq = &sa_index->genome->S[g_start + sa_index->genome->chrom_offsets[chrom] + 1];
doscadfun_inv(r_seq, r_len, g_seq, g_len, MISMATCH_PERC,
alig_out);
}