void bwa_cal_pac_pos(const char *prefix, int n_seqs, bwa_seq_t *seqs, int max_mm, float fnr)
{
int i, j;
char str[1024];
bwt_t *bwt;
// load forward SA
strcpy(str, prefix); strcat(str, ".bwt"); bwt = bwt_restore_bwt(str,0);
strcpy(str, prefix); strcat(str, ".sa"); bwt_restore_sa(str,bwt,0);
for (i = 0; i != n_seqs; ++i) {
if (seqs[i].strand) bwa_cal_pac_pos_core(bwt, 0, &seqs[i], max_mm, fnr);
for (j = 0; j < seqs[i].n_multi; ++j) {
bwt_multi1_t *p = seqs[i].multi + j;
if (p->strand) p->pos = bwt_sa(bwt, p->pos);
}
}
bwt_destroy(bwt);
// load reverse BWT and SA
strcpy(str, prefix); strcat(str, ".rbwt"); bwt = bwt_restore_bwt(str,0);
strcpy(str, prefix); strcat(str, ".rsa"); bwt_restore_sa(str,bwt,0);
for (i = 0; i != n_seqs; ++i) {
if (!seqs[i].strand) bwa_cal_pac_pos_core(0, bwt, &seqs[i], max_mm, fnr);
for (j = 0; j < seqs[i].n_multi; ++j) {
bwt_multi1_t *p = seqs[i].multi + j;
if (!p->strand) p->pos = bwt->seq_len - (bwt_sa(bwt, p->pos) + seqs[i].len);
}
}
bwt_destroy(bwt);
}
void jigsaw_cal_pac_pos (const bwt_t *bwt, bwa_seq_t *seq, int max_mm, float fnr, const int *g_log_n)
{
int j;
bwa_cal_pac_pos_core(bwt, seq, max_mm, fnr, g_log_n);
for (j = 0; j < seq->n_multi; ++j) {
bwt_multi1_t *p = seq->multi + j;
p->pos = bwt_sa(bwt, p->pos);
}
}
void bwa_cal_pac_pos(const bntseq_t *bns, const char *prefix, int n_seqs, bwa_seq_t *seqs, int max_mm, float fnr)
{
int i, j, strand, n_multi;
char str[1024];
bwt_t *bwt;
// load forward SA
strcpy(str, prefix); strcat(str, ".bwt"); bwt = bwt_restore_bwt(str);
strcpy(str, prefix); strcat(str, ".sa"); bwt_restore_sa(str, bwt);
for (i = 0; i != n_seqs; ++i) {
bwa_seq_t *p = &seqs[i];
bwa_cal_pac_pos_core(bns, bwt, p, max_mm, fnr);
for (j = n_multi = 0; j < p->n_multi; ++j) {
bwt_multi1_t *q = p->multi + j;
q->pos = bwa_sa2pos(bns, bwt, q->pos, p->len, &strand);
q->strand = strand;
if (q->pos != p->pos)
p->multi[n_multi++] = *q;
}
p->n_multi = n_multi;
}
bwt_destroy(bwt);
}
Alignment BWA::generate_final_alignment_from_sequence(bwa_seq_t* sequence) {
// Calculate the local coordinate and local alignment.
bwa_cal_pac_pos_core(bwts[0],bwts[1],sequence,options.max_diff,options.fnr);
bwa_refine_gapped(bns, 1, sequence, reference, NULL);
// Copy the local alignment data into the alignment object.
Alignment alignment;
// Populate basic path info
alignment.edit_distance = sequence->nm;
alignment.num_mismatches = sequence->n_mm;
alignment.num_gap_opens = sequence->n_gapo;
alignment.num_gap_extensions = sequence->n_gape;
alignment.num_best = sequence->c1;
alignment.num_second_best = sequence->c2;
// Final alignment position.
alignment.type = sequence->type;
bns_coor_pac2real(bns, sequence->pos, pos_end(sequence) - sequence->pos, &alignment.contig);
alignment.pos = sequence->pos - bns->anns[alignment.contig].offset + 1;
alignment.negative_strand = sequence->strand;
alignment.mapping_quality = sequence->mapQ;
// Cigar step.
alignment.cigar = NULL;
if(sequence->cigar) {
alignment.cigar = new uint16_t[sequence->n_cigar];
memcpy(alignment.cigar,sequence->cigar,sequence->n_cigar*sizeof(uint16_t));
}
alignment.n_cigar = sequence->n_cigar;
// MD tag with a better breakdown of differences in the cigar
alignment.md = strdup(sequence->md);
delete[] sequence->md;
sequence->md = NULL;
return alignment;
}
