--- /dev/null
+#include <math.h>
+#include <stdlib.h>
+#include "bam_mcns.h"
+
+#define MC_MIN_QUAL 20
+#define MC_MAX_SUMQ 3000
+#define MC_MAX_SUMQP 1e-300
+
+struct __mc_aux_t {
+ int n, N;
+ int ref, alt;
+ double *q2p, *pdg; // pdg -> P(D|g)
+ int *qsum, *bcnt;
+};
+
+mc_aux_t *mc_init(int n) // FIXME: assuming diploid
+{
+ mc_aux_t *ma;
+ int i;
+ ma = calloc(1, sizeof(mc_aux_t));
+ ma->n = n; ma->N = 2 * n;
+ ma->q2p = calloc(MC_MAX_SUMQ + 1, sizeof(double));
+ ma->qsum = calloc(4 * ma->n, sizeof(int));
+ ma->bcnt = calloc(4 * ma->n, sizeof(int));
+ ma->pdg = calloc(3 * ma->n, sizeof(double));
+ for (i = 0; i <= MC_MAX_SUMQ; ++i)
+ ma->q2p[i] = pow(10., -i / 10.);
+ return ma;
+}
+
+void mc_destroy(mc_aux_t *ma)
+{
+ if (ma) {
+ free(ma->qsum); free(ma->bcnt);
+ free(ma->q2p); free(ma->pdg);
+ free(ma);
+ }
+}
+
+static void sum_err(int *n, const bam_pileup1_t **plp, mc_aux_t *ma)
+{
+ int i, j;
+ memset(ma->qsum, 0, sizeof(int) * 4 * ma->n);
+ memset(ma->bcnt, 0, sizeof(int) * 4 * ma->n);
+ for (j = 0; j < ma->n; ++j) {
+ int *qsum = ma->qsum + j * 4;
+ int *bcnt = ma->bcnt + j * 4;
+ for (i = 0; i < n[j]; ++i) {
+ const bam_pileup1_t *p = plp[j] + i;
+ int q, b;
+ if (p->is_del || (p->b->core.flag&BAM_FUNMAP)) continue;
+ q = bam1_qual(p->b)[p->qpos];
+ if (p->b->core.qual < q) q = p->b->core.qual;
+ if (q < MC_MIN_QUAL) continue; // small qual
+ b = bam_nt16_nt4_table[(int)bam1_seqi(bam1_seq(p->b), p->qpos)];
+ if (b > 3) continue; // N
+ qsum[b] += q;
+ ++bcnt[b];
+ }
+ }
+}
+
+static void set_allele(int ref, mc_aux_t *ma)
+{
+ int i, j, sum[4], tmp;
+ sum[0] = sum[1] = sum[2] = sum[3] = 0;
+ for (i = 0; i < ma->n; ++i)
+ for (j = 0; j < 4; ++j)
+ sum[j] += ma->qsum[i * 4 + j];
+ for (j = 0; j < 4; ++j) sum[j] = sum[j]<<2 | j;
+ for (i = 1; i < 4; ++i) // insertion sort
+ for (j = i; j > 0 && sum[j] < sum[j-1]; --j)
+ tmp = sum[j], sum[j] = sum[j-1], sum[j-1] = tmp;
+ ma->ref = sum[3]&3; ma->alt = sum[2]&3;
+ if (ref == ma->alt) tmp = ma->ref, ma->ref = ma->alt, ma->alt = tmp;
+ // note that ma->ref might not be ref in case of triallele
+}
+
+static void cal_pdg(mc_aux_t *ma)
+{
+ int i, j;
+ for (j = 0; j < ma->n; ++j) {
+ int pi[3], *qsum, *bcnt;
+ double *pdg = ma->pdg + j * 3;
+ qsum = ma->qsum + j * 4;
+ bcnt = ma->bcnt + j * 4;
+ pi[1] = 3 * (bcnt[ma->ref] + bcnt[ma->alt]);
+ pi[0] = qsum[ma->alt];
+ pi[2] = qsum[ma->ref];
+ for (i = 0; i < 3; ++i)
+ pdg[i] = pi[i] < MC_MAX_SUMQ? MC_MAX_SUMQP : ma->q2p[pi[i]];
+ }
+}
+
+double mc_freq0(int ref, int *n, const bam_pileup1_t **plp, mc_aux_t *ma, int *_ref, int *alt)
+{
+ int i, acnt[4], j;
+ double f0;
+ sum_err(n, plp, ma);
+ set_allele(ref, ma);
+ cal_pdg(ma);
+ acnt[0] = acnt[1] = acnt[2] = acnt[3] = 0;
+ for (i = 0; i < ma->n; ++i)
+ for (j = 0; j < 4; ++j)
+ acnt[j] += ma->bcnt[i * 4 + j];
+ f0 = acnt[ma->ref] + acnt[ma->alt] == 0? -1.
+ : (double)acnt[ref] / (acnt[ma->ref] + acnt[ma->alt]);
+ *_ref = ma->ref; *alt = ma->alt;
+ return f0;
+}
+
+double mc_freq_iter(double f0, mc_aux_t *ma)
+{
+ double f, f3[3];
+ int i, j;
+ f3[0] = f0*f0; f3[1] = 2.*f0*(1.-f0); f3[2] = (1.-f0)*(1.-f0);
+ for (i = 0, f = 0.; i < ma->n; ++i) {
+ double up, dn, *pdg;
+ pdg = ma->pdg + i * 3;
+ for (j = 1, up = 0.; j < 3; ++j)
+ up += j * pdg[j] * f3[j];
+ for (j = 0, dn = 0.; j < 3; ++j)
+ dn += pdg[j] * f3[j];
+ f += up / dn;
+ }
+ return f;
+}
#include "sam.h"
#include "faidx.h"
#include "bam_maqcns.h"
+#include "bam_mcns.h"
#include "khash.h"
#include "glf.h"
#include "kstring.h"
***********/
typedef struct {
+ int vcf, max_mq, min_mq;
char *reg, *fn_pos;
faidx_t *fai;
kh_64_t *hash;
typedef struct {
bamFile fp;
bam_iter_t iter;
+ int min_mq;
} mplp_aux_t;
static int mplp_func(void *data, bam1_t *b)
{
mplp_aux_t *ma = (mplp_aux_t*)data;
- if (ma->iter) return bam_iter_read(ma->fp, ma->iter, b);
- return bam_read1(ma->fp, b);
+ int ret;
+ do {
+ ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b);
+ } while (b->core.qual < ma->min_mq && ret >= 0);
+ return ret;
}
static int mpileup(mplp_conf_t *conf, int n, char **fn)
{
mplp_aux_t **data;
+ mc_aux_t *ma = 0;
int i, tid, pos, *n_plp, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid;
const bam_pileup1_t **plp;
bam_mplp_t iter;
for (i = 0; i < n; ++i) {
bam_header_t *h_tmp;
data[i] = calloc(1, sizeof(mplp_aux_t));
+ data[i]->min_mq = conf->min_mq;
data[i]->fp = bam_open(fn[i], "r");
h_tmp = bam_header_read(data[i]->fp);
if (conf->reg) {
}
}
if (conf->fn_pos) hash = load_pos(conf->fn_pos, h);
+ // write the VCF header
+ if (conf->vcf) {
+ kstring_t s;
+ s.l = s.m = 0; s.s = 0;
+ kputs("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT", &s);
+ for (i = 0; i < n; ++i) {
+ const char *p;
+ kputc('\t', &s);
+ if ((p = strstr(fn[i], ".bam")) != 0)
+ kputsn(fn[i], p - fn[i], &s);
+ else kputs(fn[i], &s);
+ }
+ puts(s.s);
+ free(s.s);
+ }
// mpileup
+ if (conf->vcf) ma = mc_init(n);
ref_tid = -1; ref = 0;
iter = bam_mplp_init(n, mplp_func, (void**)data);
while (bam_mplp_auto(iter, &tid, &pos, n_plp, plp) > 0) {
if (conf->fai) ref = fai_fetch(conf->fai, h->target_name[tid], &ref_len);
ref_tid = tid;
}
- printf("%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');
- for (i = 0; i < n; ++i) {
- int j;
- printf("\t%d\t", n_plp[i]);
- if (n_plp[i] == 0) printf("*\t*");
- else {
- for (j = 0; j < n_plp[i]; ++j)
- pileup_seq(plp[i] + j, pos, ref_len, ref);
- putchar('\t');
+ if (conf->vcf) {
+ double f;
+ int j, _ref, _alt, _ref0, depth, rms_q;
+ uint64_t sqr_sum;
+ _ref0 = (ref && pos < ref_len)? ref[pos] : 'N';
+ _ref0 = bam_nt16_nt4_table[bam_nt16_table[_ref0]];
+ f = mc_freq0(_ref0, n_plp, plp, ma, &_ref, &_alt);
+ printf("%s\t%d\t.\t%c\t", h->target_name[tid], pos + 1, "ACGTN"[_ref0]);
+ if (_ref0 == _ref) putchar("ACGTN"[_alt]);
+ else printf("%c,%c", "ACGTN"[_ref], "ACGTN"[_alt]);
+ printf("\t0\tPASS\t"); // FIXME: currently these not available
+ for (i = depth = 0, sqr_sum = 0; i < n; ++i) {
+ depth += n_plp[i];
for (j = 0; j < n_plp[i]; ++j) {
- const bam_pileup1_t *p = plp[i] + j;
- int c = bam1_qual(p->b)[p->qpos] + 33;
- if (c > 126) c = 126;
- putchar(c);
+ int q = plp[i][j].b->core.qual;
+ if (q > conf->max_mq) q = conf->max_mq;
+ sqr_sum += q * q;
+ }
+ }
+ rms_q = (int)(sqrt((double)sqr_sum / depth) + .499);
+ printf("DP=%d;MQ=%d;AF=%.3lg", depth, rms_q, 1.-f); // FIXME: not working for triallelic alleles
+ printf("\tDP");
+ // output genotype information; FIXME: to be implmented...
+ for (i = 0; i < n; ++i)
+ printf("\t%d", n_plp[i]);
+ putchar('\n');
+ } else {
+ printf("%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');
+ for (i = 0; i < n; ++i) {
+ int j;
+ printf("\t%d\t", n_plp[i]);
+ if (n_plp[i] == 0) printf("*\t*");
+ else {
+ for (j = 0; j < n_plp[i]; ++j)
+ pileup_seq(plp[i] + j, pos, ref_len, ref);
+ putchar('\t');
+ for (j = 0; j < n_plp[i]; ++j) {
+ const bam_pileup1_t *p = plp[i] + j;
+ int c = bam1_qual(p->b)[p->qpos] + 33;
+ if (c > 126) c = 126;
+ putchar(c);
+ }
}
}
+ putchar('\n');
}
- putchar('\n');
}
if (hash) { // free the hash table
khint_t k;
if (kh_exist(hash, k)) free(kh_val(hash, k));
kh_destroy(64, hash);
}
+ mc_destroy(ma);
bam_mplp_destroy(iter);
bam_header_destroy(h);
for (i = 0; i < n; ++i) {
int c;
mplp_conf_t mplp;
memset(&mplp, 0, sizeof(mplp_conf_t));
- while ((c = getopt(argc, argv, "f:r:l:")) >= 0) {
+ mplp.max_mq = 60;
+ while ((c = getopt(argc, argv, "f:r:l:VM:q:")) >= 0) {
switch (c) {
case 'f':
mplp.fai = fai_load(optarg);
break;
case 'r': mplp.reg = strdup(optarg); break;
case 'l': mplp.fn_pos = strdup(optarg); break;
+ case 'V': mplp.vcf = 1; break;
+ case 'M': mplp.max_mq = atoi(optarg); break;
+ case 'q': mplp.min_mq = atoi(optarg); break;
}
}
if (argc == 1) {
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