#include "sam.h"
#include "kstring.h"
#include "kaln.h"
+#include "kprobaln.h"
void bam_fillmd1_core(bam1_t *b, char *ref, int is_equal, int max_nm)
{
return (int)(t + .499);
}
-// local realignment
-
-#define MIN_REF_LEN 10
-#define MIN_BAND_WIDTH 11
-
-int bam_realn(bam1_t *b, const char *ref)
-{
- int k, score, q[2], r[2], kk[2], kl[2], x, y, max, j, n_cigar, endx = -1;
- uint32_t *cigar = bam1_cigar(b);
- uint8_t *seq = bam1_seq(b);
- bam1_core_t *c = &b->core;
- q[0] = q[1] = r[0] = r[1] = kk[0] = kk[1] = kl[0] = kl[1] = -1;
- // find the right boundary
- for (k = 0, score = max = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) {
- int op = cigar[k]&0xf;
- int ol = cigar[k]>>4;
- if (op == BAM_CMATCH) {
- for (j = 0; j < ol; ++j) {
- int c1, c2, z = y + j;
- c1 = bam_nt16_nt4_table[bam1_seqi(seq, z)];
- if (ref[x+j] == 0) return -1;
- c2 = bam_nt16_nt4_table[(int)bam_nt16_table[(int)ref[x+j]]];
- if (c1 < 3 && c2 < 3)
- score += c1 == c2? 5 : -4;
- if (score < 0) score = 0;
- if (score > max) max = score, q[1] = z, r[1] = x+j, kk[1] = k, kl[1] = j + 1;
- }
- x += ol; y += ol;
- } else if (op == BAM_CINS) {
- score -= 4 - ol * 3;
- y += ol;
- if (score < 0) score = 0;
- } else if (op == BAM_CDEL) {
- score -= 4 - ol * 3;
- x += ol;
- if (score < 0) score = 0;
- } else if (op == BAM_CSOFT_CLIP) y += ol;
- else if (op == BAM_CREF_SKIP) x += ol;
- }
- if (q[1] < 0) return -1; // no high scoring segments
- endx = x - 1;
- // find the left boundary
- for (k = c->n_cigar - 1, score = max = 0, x = x-1, y = y-1; k >= 0; --k) {
- int op = cigar[k]&0xf;
- int ol = cigar[k]>>4;
- if (op == BAM_CMATCH) {
- for (j = 0; j < ol; ++j) {
- int c1, c2, z = y - j;
- c1 = bam_nt16_nt4_table[bam1_seqi(seq, z)];
- if (ref[x+j] == 0) return -1;
- c2 = bam_nt16_nt4_table[(int)bam_nt16_table[(int)ref[x-j]]];
- if (c1 < 3 && c2 < 3)
- score += c1 == c2? 5 : -4;
- if (score < 0) score = 0;
- if (score > max) max = score, q[0] = z, r[0] = x-j, kk[0] = k, kl[0] = j + 1;
- }
- x -= ol; y -= ol;
- } else if (op == BAM_CINS) {
- score -= 4 - ol * 3;
- y -= ol;
- if (score < 0) score = 0;
- } else if (op == BAM_CDEL) {
- score -= 4 - ol * 3;
- x -= ol;
- if (score < 0) score = 0;
- } else if (op == BAM_CSOFT_CLIP) y -= ol;
- else if (op == BAM_CREF_SKIP) x -= ol;
- }
- if (q[0] < 0 || q[1] - q[0] < 15) return -1; // the high-scoring segment is too short
- // modify CIGAR
- n_cigar = 0;
- cigar = calloc(c->n_cigar + 4, 4);
- if (q[0] != 0) cigar[n_cigar++] = (uint32_t)q[0]<<4 | BAM_CSOFT_CLIP;
- if (r[0] != c->pos) cigar[n_cigar++] = (uint32_t)(r[0] - c->pos)<<4 | BAM_CREF_SKIP;
- if (kk[0] == kk[1]) {
- cigar[n_cigar++] = (uint32_t)(kl[0] + kl[1] - (bam1_cigar(b)[kk[0]]>>4))<<4 | BAM_CMATCH;
- } else {
- cigar[n_cigar++] = (uint32_t)kl[0]<<4 | BAM_CMATCH;
- for (k = kk[0] + 1; k < kk[1]; ++k)
- cigar[n_cigar++] = bam1_cigar(b)[k];
- cigar[n_cigar++] = (uint32_t)kl[1]<<4 | BAM_CMATCH; // FIXME: add ref_skip after this line
- }
- if (q[1] + 1 != c->l_qseq)
- cigar[n_cigar++] = (uint32_t)(c->l_qseq - q[1] - 1)<<4 | BAM_CSOFT_CLIP;
- // copy over the alignment
- if (4 * (n_cigar - (int)c->n_cigar) + b->data_len > b->m_data) { // enlarge b->data
- b->m_data = 4 * (n_cigar - (int)c->n_cigar) + b->data_len;
- kroundup32(b->m_data);
- b->data = realloc(b->data, b->m_data);
- }
- if (n_cigar != (int)c->n_cigar) { // move data
- memmove(b->data + c->l_qname + 4 * n_cigar, bam1_seq(b), b->data_len - c->l_qname - 4 * c->n_cigar);
- b->data_len += 4 * (n_cigar - (int)c->n_cigar);
- }
- memcpy(bam1_cigar(b), cigar, n_cigar * 4);
- c->n_cigar = n_cigar;
- free(cigar);
- return 0;
-}
-
-int bam_prob_realn(bam1_t *b, const char *ref)
+int bam_prob_realn_core(bam1_t *b, const char *ref, int write_bq)
{
int k, i, bw, x, y, yb, ye, xb, xe;
uint32_t *cigar = bam1_cigar(b);
bam1_core_t *c = &b->core;
- ka_probpar_t conf = ka_probpar_def;
- // find the start and end of the alignment
+ kpa_par_t conf = kpa_par_def;
if (c->flag & BAM_FUNMAP) return -1;
+ if (bam_aux_get(b, "BQ")) return -2;
+ // find the start and end of the alignment
x = c->pos, y = 0, yb = ye = xb = xe = -1;
for (k = 0; k < c->n_cigar; ++k) {
int op, l;
if (xe - xb - c->l_qseq > bw)
xb += (xe - xb - c->l_qseq - bw) / 2, xe -= (xe - xb - c->l_qseq - bw) / 2;
{ // glocal
- uint8_t *s, *r, *q, *seq = bam1_seq(b), *qual = bam1_qual(b);
+ uint8_t *s, *r, *q, *seq = bam1_seq(b), *qual = bam1_qual(b), *bq = 0;
int *state;
+ if (write_bq) {
+ bq = calloc(c->l_qseq + 1, 1);
+ memcpy(bq, qual, c->l_qseq);
+ }
s = calloc(c->l_qseq, 1);
for (i = 0; i < c->l_qseq; ++i) s[i] = bam_nt16_nt4_table[bam1_seqi(seq, i)];
r = calloc(xe - xb, 1);
r[i-xb] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[i]]];
state = calloc(c->l_qseq, sizeof(int));
q = calloc(c->l_qseq, 1);
- ka_prob_glocal(r, xe-xb, s, c->l_qseq, qual, &conf, state, q);
+ kpa_glocal(r, xe-xb, s, c->l_qseq, qual, &conf, state, q);
for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) {
int op = cigar[k]&0xf, l = cigar[k]>>4;
if (op == BAM_CMATCH) {
} else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l;
else if (op == BAM_CDEL) x += l;
}
+ if (write_bq) {
+ for (i = 0; i < c->l_qseq; ++i) bq[i] = bq[i] - qual[i] + 33;
+ bam_aux_append(b, "BQ", 'Z', c->l_qseq + 1, bq);
+ free(bq);
+ }
free(s); free(r); free(q); free(state);
}
return 0;
}
+int bam_prob_realn(bam1_t *b, const char *ref)
+{
+ return bam_prob_realn_core(b, ref, 0);
+}
+
int bam_fillmd(int argc, char *argv[])
{
int c, is_equal = 0, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed, max_nm = 0, is_realn, capQ = 0;
fprintf(stderr, "[bam_fillmd] fail to find sequence '%s' in the reference.\n",
fp->header->target_name[tid]);
}
-// if (is_realn) bam_realn(b, ref);
- if (is_realn) bam_prob_realn(b, ref);
+ if (is_realn) bam_prob_realn_core(b, ref, 1);
if (capQ > 10) {
int q = bam_cap_mapQ(b, ref, capQ);
if (b->core.qual > q) b->core.qual = q;