/*band_width: band width for dynamic programming*/
void jigsaw_refine_gapped(int64_t l_pac, bwa_seq_t *seq, const ubyte_t *pacseq, const ubyte_t *ntpac, int band_width)
{
int j;
kstring_t *str;
bwa_seq_t *s = seq;
//uint32_t pos = s->pos; //debug
for (j = 0; j < s->n_multi; ++j) {
bwt_multi1_t *q = s->multi + j;
int n_cigar;
if (q->gap_t + q->gap_q == 0) continue;
int seq_len_t = s->len + q->gap_q - q->gap_t;
q->cigar = refine_gapped_core(l_pac, pacseq, s->len, q->strand? s->rseq : s->seq, &q->pos,
seq_len_t, &n_cigar, band_width);
q->n_cigar = n_cigar;
}
if (s->type != BWA_TYPE_NO_MATCH && s->type != BWA_TYPE_MATESW && s->n_gapo_t + s->n_gapo_q != 0){
int seq_len_t = s->len + s->n_gapo_q + s->n_gape_q - s->n_gapo_t - s->n_gape_t;
s->cigar = refine_gapped_core(l_pac, pacseq, s->len, s->strand? s->rseq : s->seq, &s->pos,
seq_len_t, &s->n_cigar, band_width);
}
if (ntpac) { // in color space
bwa_cs2nt_core(s, l_pac, ntpac);
for (j = 0; j < s->n_multi; ++j) {
bwt_multi1_t *q = s->multi + j;
int n_cigar;
if (q->gap_t + q->gap_q == 0) continue;
free(q->cigar);
int seq_len_t = s->len + q->gap_q - q->gap_t;
q->cigar = refine_gapped_core(l_pac, ntpac, s->len, q->strand? s->rseq : s->seq, &q->pos,
seq_len_t, &n_cigar, band_width);
q->n_cigar = n_cigar;
}
if (s->type != BWA_TYPE_NO_MATCH && s->cigar) { // update cigar again
free(s->cigar);
int seq_len_t = s->len + s->n_gapo_q + s->n_gape_q - s->n_gapo_t - s->n_gape_t;
s->cigar = refine_gapped_core(l_pac, ntpac, s->len, s->strand? s->rseq : s->seq, &s->pos,
seq_len_t, &s->n_cigar, band_width);
}
}
// generate MD tag
str = (kstring_t*)calloc(1, sizeof(kstring_t));
if (s->type != BWA_TYPE_NO_MATCH) {
int nm;
s->md = bwa_cal_md1(s->n_cigar, s->cigar, s->len, s->pos, s->strand? s->rseq : s->seq,
l_pac, ntpac? ntpac : pacseq, str, &nm);
s->nm = nm;
}
free(str->s); free(str);
// correct for trimmed reads
if (!ntpac) // trimming is only enabled for Illumina reads
bwa_correct_trimmed(s);
}
void bwa_rg_tpx(int iidx, const bntseq_t *bns, int n_seqs1, int n_seqs2,
bwa_seq_t *seqs, ubyte_t *pacseq, bntseq_t *ntbns)
{
ubyte_t *ntpac = 0;
int i, j;
kstring_t *str;
#ifdef _TIMING
struct timeval st;
uint64_t s1, e1;
double pos1_time = 0.0;
#endif
#ifdef _TIMING
gettimeofday(&st, NULL);
s1 = st.tv_sec * 1000000L + (time_t)st.tv_usec;
#endif
for (i = n_seqs1; i < n_seqs2; ++i) {
bwa_seq_t *s = seqs + i;
seq_reverse(s->len, s->seq, 0); // IMPORTANT: s->seq is reversed here!!!
for (j = 0; j < s->n_multi; ++j) {
bwt_multi1_t *q = s->multi + j;
int n_cigar;
if (q->gap == 0) continue;
q->cigar = refine_gapped_core(bns->l_pac, pacseq, s->len, q->strand? s->rseq : s->seq, &q->pos,
(q->strand? 1 : -1) * q->gap, &n_cigar, 1);
q->n_cigar = n_cigar;
}
if (s->type == BWA_TYPE_NO_MATCH || s->type == BWA_TYPE_MATESW || s->n_gapo == 0) continue;
s->cigar = refine_gapped_core(bns->l_pac, pacseq, s->len, s->strand? s->rseq : s->seq, &s->pos,
(s->strand? 1 : -1) * (s->n_gapo + s->n_gape), &s->n_cigar, 1);
}
if (ntbns) { // in color space
for (i = n_seqs1; i < n_seqs2; ++i) {
bwa_seq_t *s = seqs + i;
bwa_cs2nt_core(s, bns->l_pac, ntpac);
for (j = 0; j < s->n_multi; ++j) {
bwt_multi1_t *q = s->multi + j;
int n_cigar;
if (q->gap == 0) continue;
free(q->cigar);
q->cigar = refine_gapped_core(bns->l_pac, ntpac, s->len, q->strand? s->rseq : s->seq, &q->pos,
(q->strand? 1 : -1) * q->gap, &n_cigar, 0);
q->n_cigar = n_cigar;
}
if (s->type != BWA_TYPE_NO_MATCH && s->cigar) { // update cigar again
free(s->cigar);
s->cigar = refine_gapped_core(bns->l_pac, ntpac, s->len, s->strand? s->rseq : s->seq, &s->pos,
(s->strand? 1 : -1) * (s->n_gapo + s->n_gape), &s->n_cigar, 0);
}
}
}
// generate MD tag
str = (kstring_t*)calloc(1, sizeof(kstring_t));
for (i = n_seqs1; i < n_seqs2; ++i) {
bwa_seq_t *s = seqs + i;
if (s->type != BWA_TYPE_NO_MATCH) {
int nm;
s->md = bwa_cal_md1(s->n_cigar, s->cigar, s->len, s->pos, s->strand? s->rseq : s->seq,
bns->l_pac, ntbns? ntpac : pacseq, str, &nm);
s->nm = nm;
}
}
free(str->s); free(str);
// correct for trimmed reads
if (!ntbns) // trimming is only enabled for Illumina reads
for (i = n_seqs1; i < n_seqs2; ++i) bwa_correct_trimmed(seqs + i);
#ifdef _TIMING
gettimeofday(&st, NULL);
e1 = st.tv_sec * 1000000L + (time_t)st.tv_usec;
pos1_time = (double)((double)e1 - (double)s1) / 1000000.0;
# ifdef HAVE_PTHREAD
pthread_mutex_lock(&pe_lock);
# endif // HAVE_PTHREAD
fprintf(stderr,"bwapese1 time = %lf (sec)\n",pos1_time);
# ifdef HAVE_PTHREAD
pthread_mutex_unlock(&pe_lock);
# endif // HAVE_PTHREAD
#endif
return;
}