#include "sam.h"
#include "kstring.h"
#include "kaln.h"
+#include "kprobaln.h"
+
+char bam_nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };
void bam_fillmd1_core(bam1_t *b, char *ref, int is_equal, int max_nm)
{
return (int)(t + .499);
}
-int bam_prob_realn(bam1_t *b, const char *ref)
+int bam_prob_realn_core(bam1_t *b, const char *ref, int flag)
{
- int k, i, bw, x, y, yb, ye, xb, xe;
+ int k, i, bw, x, y, yb, ye, xb, xe, apply_baq = flag&1, extend_baq = flag>>1&1;
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
- if (c->flag & BAM_FUNMAP) return -1;
+ kpa_par_t conf = kpa_par_def;
+ uint8_t *bq = 0, *zq = 0, *qual = bam1_qual(b);
+ if ((c->flag & BAM_FUNMAP) || b->core.l_qseq == 0) return -1; // do nothing
+ // test if BQ or ZQ is present
+ if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq;
+ if ((zq = bam_aux_get(b, "ZQ")) != 0 && *zq == 'Z') ++zq;
+ if (bq && zq) { // remove the ZQ tag
+ bam_aux_del(b, zq-1);
+ zq = 0;
+ }
+ if (bq || zq) {
+ if ((apply_baq && zq) || (!apply_baq && bq)) return -3; // in both cases, do nothing
+ if (bq && apply_baq) { // then convert BQ to ZQ
+ for (i = 0; i < c->l_qseq; ++i)
+ qual[i] = qual[i] + 64 < bq[i]? 0 : qual[i] - ((int)bq[i] - 64);
+ *(bq - 3) = 'Z';
+ } else if (zq && !apply_baq) { // then convert ZQ to BQ
+ for (i = 0; i < c->l_qseq; ++i)
+ qual[i] += (int)zq[i] - 64;
+ *(zq - 3) = 'B';
+ }
+ return 0;
+ }
+ // 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;
x += l; y += l;
} else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l;
else if (op == BAM_CDEL) x += l;
- else if (op == BAM_CREF_SKIP) return -1;
+ else if (op == BAM_CREF_SKIP) return -1; // do nothing if there is a reference skip
}
// set bandwidth and the start and the end
bw = 7;
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), *bq;
int *state;
+ 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);
- for (i = xb; i < xe; ++i)
+ for (i = xb; i < xe; ++i) {
+ if (ref[i] == 0) { xe = i; break; }
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);
- 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) {
- for (i = y; i < y + l; ++i) {
- if ((state[i]&3) != 0 || state[i]>>2 != x - xb + (i - y)) qual[i] = 0;
- else qual[i] = qual[i] < q[i]? qual[i] : q[i];
- }
- x += l; y += l;
- } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l;
- else if (op == BAM_CDEL) x += l;
+ kpa_glocal(r, xe-xb, s, c->l_qseq, qual, &conf, state, q);
+ if (!extend_baq) { // in this block, bq[] is capped by base quality qual[]
+ 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) {
+ for (i = y; i < y + l; ++i) {
+ if ((state[i]&3) != 0 || state[i]>>2 != x - xb + (i - y)) bq[i] = 0;
+ else bq[i] = bq[i] < q[i]? bq[i] : q[i];
+ }
+ x += l; y += l;
+ } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l;
+ else if (op == BAM_CDEL) x += l;
+ }
+ for (i = 0; i < c->l_qseq; ++i) bq[i] = qual[i] - bq[i] + 64; // finalize BQ
+ } else { // in this block, bq[] is BAQ that can be larger than qual[] (different from the above!)
+ uint8_t *left, *rght;
+ left = calloc(c->l_qseq, 1); rght = calloc(c->l_qseq, 1);
+ 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) {
+ for (i = y; i < y + l; ++i)
+ bq[i] = ((state[i]&3) != 0 || state[i]>>2 != x - xb + (i - y))? 0 : q[i];
+ for (left[y] = bq[y], i = y + 1; i < y + l; ++i)
+ left[i] = bq[i] > left[i-1]? bq[i] : left[i-1];
+ for (rght[y+l-1] = bq[y+l-1], i = y + l - 2; i >= y; --i)
+ rght[i] = bq[i] > rght[i+1]? bq[i] : rght[i+1];
+ for (i = y; i < y + l; ++i)
+ bq[i] = left[i] < rght[i]? left[i] : rght[i];
+ x += l; y += l;
+ } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l;
+ else if (op == BAM_CDEL) x += l;
+ }
+ for (i = 0; i < c->l_qseq; ++i) bq[i] = 64 + (qual[i] <= bq[i]? 0 : qual[i] - bq[i]); // finalize BQ
+ free(left); free(rght);
}
- free(s); free(r); free(q); free(state);
+ if (apply_baq) {
+ for (i = 0; i < c->l_qseq; ++i) qual[i] -= bq[i] - 64; // modify qual
+ bam_aux_append(b, "ZQ", 'Z', c->l_qseq + 1, bq);
+ } else 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, 1);
+}
+
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;
+ int c, is_equal, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed, max_nm, is_realn, capQ, baq_flag;
samfile_t *fp, *fpout = 0;
faidx_t *fai;
char *ref = 0, mode_w[8], mode_r[8];
bam1_t *b;
- is_bam_out = is_sam_in = is_uncompressed = is_realn = 0;
+ is_equal = is_bam_out = is_sam_in = is_uncompressed = is_realn = max_nm = capQ = baq_flag = 0;
mode_w[0] = mode_r[0] = 0;
strcpy(mode_r, "r"); strcpy(mode_w, "w");
- while ((c = getopt(argc, argv, "reubSC:n:")) >= 0) {
+ while ((c = getopt(argc, argv, "EreubSC:n:A")) >= 0) {
switch (c) {
case 'r': is_realn = 1; break;
case 'e': is_equal = 1; break;
case 'S': is_sam_in = 1; break;
case 'n': max_nm = atoi(optarg); break;
case 'C': capQ = atoi(optarg); break;
+ case 'A': baq_flag |= 1; break;
+ case 'E': baq_flag |= 2; break;
default: fprintf(stderr, "[bam_fillmd] unrecognized option '-%c'\n", c); return 1;
}
}
fprintf(stderr, " -u uncompressed BAM output (for piping)\n");
fprintf(stderr, " -b compressed BAM output\n");
fprintf(stderr, " -S the input is SAM with header\n");
- fprintf(stderr, " -r read-independent local realignment\n\n");
+ fprintf(stderr, " -A modify the quality string\n");
+ fprintf(stderr, " -r compute the BQ tag (without -A) or cap baseQ by BAQ (with -A)\n");
+ fprintf(stderr, " -E extended BAQ for better sensitivity but lower specificity\n\n");
return 1;
}
fp = samopen(argv[optind], mode_r, 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, baq_flag);
if (capQ > 10) {
int q = bam_cap_mapQ(b, ref, capQ);
if (b->core.qual > q) b->core.qual = q;
projects / samtools.git / blobdiff