#include <stdlib.h>
#include "bam_mcns.h"
-#define MC_MIN_QUAL 20
+#define MC_MIN_QUAL 13
#define MC_MAX_SUMQ 3000
#define MC_MAX_SUMQP 1e-300
int n, N;
int ref, alt;
double *q2p, *pdg; // pdg -> P(D|g)
- int *qsum, *bcnt;
+ int *qsum, *bcnt, rcnt[4];
};
mc_aux_t *mc_init(int n) // FIXME: assuming diploid
int i, j;
memset(ma->qsum, 0, sizeof(int) * 4 * ma->n);
memset(ma->bcnt, 0, sizeof(int) * 4 * ma->n);
+ memset(ma->rcnt, 0, sizeof(int) * 4);
for (j = 0; j < ma->n; ++j) {
- int *qsum = ma->qsum + j * 4;
+ int tmp, *qsum = ma->qsum + j * 4;
int *bcnt = ma->bcnt + j * 4;
- for (i = 0; i < n[j]; ++i) {
+ double r = drand48(), rr;
+ for (i = tmp = 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;
if (b > 3) continue; // N
qsum[b] += q;
++bcnt[b];
+ ++tmp;
+ }
+ if (tmp) {
+ for (i = 0, rr = 0.; i < 4; ++i) {
+ rr += (double)bcnt[i] / tmp;
+ if (rr >= r) break;
+ }
+ if (i < 4) ++ma->rcnt[i];
}
}
}
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];
+ pi[0] = qsum[ma->ref];
+ pi[2] = qsum[ma->alt];
for (i = 0; i < 3; ++i)
- pdg[i] = pi[i] < MC_MAX_SUMQ? MC_MAX_SUMQP : ma->q2p[pi[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;
+ double fr = -1., f0 = -1.;
sum_err(n, plp, ma);
set_allele(ref, ma);
cal_pdg(ma);
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]);
+ if (ma->rcnt[ma->ref] + ma->rcnt[ma->alt]) // never used...
+ fr = (double)ma->rcnt[ref] / (ma->rcnt[ma->ref] + ma->rcnt[ma->alt]);
+ if (acnt[ma->ref] + acnt[ma->alt])
+ f0 = (double)acnt[ref] / (acnt[ma->ref] + acnt[ma->alt]);
*_ref = ma->ref; *alt = ma->alt;
- return f0;
+ return ma->n == 1 || fr < 0.? f0 : fr;
}
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);
+ f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0;
for (i = 0, f = 0.; i < ma->n; ++i) {
double up, dn, *pdg;
pdg = ma->pdg + i * 3;
dn += pdg[j] * f3[j];
f += up / dn;
}
+ f /= ma->n * 2.;
return f;
}