#include "errmod.h"
#include "bcftools/bcf.h"
-#define END_DIST_THRES 11
-
extern void ks_introsort_uint32_t(size_t n, uint32_t a[]);
#define CALL_ETA 0.03f
#define CALL_MAX 256
#define CALL_DEFTHETA 0.83f
+#define CAP_DIST 25
+
struct __bcf_callaux_t {
int max_bases, capQ, min_baseQ;
uint16_t *bases;
int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base /*4-bit*/, bcf_callaux_t *bca, bcf_callret1_t *r)
{
- int i, k, n, ref4;
+ int i, n, ref4;
memset(r, 0, sizeof(bcf_callret1_t));
ref4 = bam_nt16_nt4_table[ref_base];
if (_n == 0) return -1;
bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases);
}
// fill the bases array
- memset(r->qsum, 0, 4 * sizeof(float));
- for (i = n = 0, r->sum_Q2 = 0; i < _n; ++i) {
+ memset(r, 0, sizeof(bcf_callret1_t));
+ for (i = n = 0; i < _n; ++i) {
const bam_pileup1_t *p = pl + i;
- int q, b, mapQ;
- int min_dist;
+ int q, b, mapQ, baseQ, is_diff, min_dist;
// set base
if (p->is_del || (p->b->core.flag&BAM_FUNMAP)) continue; // skip unmapped reads and deleted bases
- q = (int)bam1_qual(p->b)[p->qpos]; // base quality
+ baseQ = q = (int)bam1_qual(p->b)[p->qpos]; // base quality
if (q < bca->min_baseQ) continue;
mapQ = p->b->core.qual < bca->capQ? p->b->core.qual : bca->capQ;
- r->sum_Q2 += mapQ * mapQ;
if (q > mapQ) q = mapQ;
if (q > 63) q = 63;
if (q < 4) q = 4;
b = bam1_seqi(bam1_seq(p->b), p->qpos); // base
b = bam_nt16_nt4_table[b? b : ref_base]; // b is the 2-bit base
bca->bases[n++] = q<<5 | (int)bam1_strand(p->b)<<4 | b;
- // collect other information
+ // collect annotations
r->qsum[b] += q;
- k = (ref4 < 4 && b == ref4)? 0 : 1;
- k = k<<1 | bam1_strand(p->b);
- ++r->d[k];
- // calculate min_dist
+ is_diff = (ref4 < 4 && b == ref4)? 0 : 1;
+ ++r->anno[0<<2|is_diff<<1|bam1_strand(p->b)];
min_dist = p->b->core.l_qseq - 1 - p->qpos;
if (min_dist > p->qpos) min_dist = p->qpos;
- k = (k&2) | (min_dist <= END_DIST_THRES);
- ++r->ed[k];
+ if (min_dist > CAP_DIST) min_dist = CAP_DIST;
+ r->anno[1<<2|is_diff<<1|0] += baseQ;
+ r->anno[1<<2|is_diff<<1|1] += baseQ * baseQ;
+ r->anno[2<<2|is_diff<<1|0] += mapQ;
+ r->anno[2<<2|is_diff<<1|1] += mapQ * mapQ;
+ r->anno[3<<2|is_diff<<1|0] += min_dist;
+ r->anno[3<<2|is_diff<<1|1] += min_dist * min_dist;
}
r->depth = n;
// glfgen
int64_t tmp;
call->ori_ref = ref4 = bam_nt16_nt4_table[ref_base];
if (ref4 > 4) ref4 = 4;
- // calculate esum
+ // calculate qsum
memset(qsum, 0, 4 * sizeof(int));
for (i = 0; i < n; ++i)
for (j = 0; j < 4; ++j)
call->shift = (int)(sum_min + .499);
}
// combine annotations
- memset(call->d, 0, 4 * sizeof(int));
- memset(call->ed, 0, 4 * sizeof(int));
+ memset(call->anno, 0, 16 * sizeof(int));
for (i = call->depth = 0, tmp = 0; i < n; ++i) {
call->depth += calls[i].depth;
- for (j = 0; j < 4; ++j) call->d[j] += calls[i].d[j], call->ed[j] += calls[i].ed[j];
- tmp += calls[i].sum_Q2;
+ for (j = 0; j < 16; ++j) call->anno[j] += calls[i].anno[j];
}
- call->rmsQ = (int)(sqrt((double)tmp / call->depth) + .499);
return 0;
}
kputc('\0', &s);
kputc('\0', &s);
// INFO
- kputs("MQ=", &s); kputw(bc->rmsQ, &s);
- kputs(";DP4=", &s);
- for (i = 0; i < 4; ++i) {
- if (i) kputc(',', &s);
- kputw(bc->d[i], &s);
- }
- kputs(";ED4=", &s);
- for (i = 0; i < 4; ++i) {
+ kputs("I16=", &s);
+ for (i = 0; i < 16; ++i) {
if (i) kputc(',', &s);
- kputw(bc->ed[i], &s);
+ kputw(bc->anno[i], &s);
}
kputc('\0', &s);
// FMT
}
/* Regularized incomplete beta function. The method is taken from
- * Numerical Recipe in C, 2nd edition, section 6.4. The following page
- * calculates the incomplete beta function, which equals
+ * Numerical Recipe in C, 2nd edition, section 6.4. The following web
+ * page calculates the incomplete beta function, which equals
* kf_betai(a,b,x) * gamma(a) * gamma(b) / gamma(a+b):
*
* http://www.danielsoper.com/statcalc/calc36.aspx
*/
static double kf_betai_aux(double a, double b, double x)
{
- double C, D, f, z;
+ double C, D, f;
int j;
+ if (x == 0.) return 0.;
+ if (x == 1.) return 1.;
f = 1.; C = f; D = 0.;
// Modified Lentz's algorithm for computing continued fraction
for (j = 1; j < 200; ++j) {
f *= d;
if (fabs(d - 1.) < KF_GAMMA_EPS) break;
}
- z = (x == 0. || x == 1.)? 0. : exp(kf_lgamma(a+b) - kf_lgamma(a) - kf_lgamma(b) + a * log(x) + b * log(1.-x));
- return z / a / f;
+ return exp(kf_lgamma(a+b) - kf_lgamma(a) - kf_lgamma(b) + a * log(x) + b * log(1.-x)) / a / f;
}
double kf_betai(double a, double b, double x)
{
return kf_gammaq(.5, chi2 / 2.);
}
-extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
+typedef struct {
+ double p[4];
+ int mq, depth, is_tested, d[4];
+} anno16_t;
-static double test_fisher(bcf1_t *b, const char *key, int d[4], int is_single)
+static double ttest(int n1, int n2, int a[4])
{
- double left, right, two;
- char *p;
+ extern double kf_betai(double a, double b, double x);
+ double t, v;
+ if (n1 == 0 || n2 == 0 || n1 + n2 < 3) return 1.0;
+ t = (a[0] / n1 - a[2] / n2) / sqrt((a[1] + a[3]) / (n1 + n2 - 2) * (1./n1 + 1./n2));
+ v = n1 + n2 - 2;
+// printf("%d,%d,%d,%d,%lf\n", a[0], a[1], a[2], a[3], t);
+ return t < 0.? 1. : .5 * kf_betai(.5*v, .5, v/(v+t*t));
+}
+
+static int test16_core(int anno[16], anno16_t *a)
+{
+ extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
+ double left, right;
int i;
- if ((p = strstr(b->info, key)) == 0) return -1.;
+ a->p[0] = a->p[1] = a->p[2] = a->p[3] = 1.;
+ memcpy(a->d, anno, 4 * sizeof(int));
+ a->depth = anno[0] + anno[1] + anno[2] + anno[3];
+ a->is_tested = (anno[0] + anno[1] > 0 && anno[2] + anno[3] > 0);
+ if (a->depth == 0) return -1;
+ a->mq = (int)(sqrt((anno[9] + anno[11]) / a->depth) + .499);
+ kt_fisher_exact(anno[0], anno[1], anno[2], anno[3], &left, &right, &a->p[0]);
+ for (i = 1; i < 4; ++i)
+ a->p[i] = ttest(anno[0] + anno[1], anno[2] + anno[3], anno+4*i);
+ return 0;
+}
+
+static int test16(bcf1_t *b, anno16_t *a)
+{
+ char *p;
+ int i, anno[16];
+ a->p[0] = a->p[1] = a->p[2] = a->p[3] = 1.;
+ a->d[0] = a->d[1] = a->d[2] = a->d[3] = 0.;
+ a->mq = a->depth = a->is_tested = 0;
+ if ((p = strstr(b->info, "I16=")) == 0) return -1;
p += 4;
- for (i = 0; i < 4; ++i) {
- d[i] = strtol(p, &p, 10);
- if (d[i] == 0 && (errno == EINVAL || errno == ERANGE)) return -2.;
+ for (i = 0; i < 16; ++i) {
+ anno[i] = strtol(p, &p, 10);
+ if (anno[i] == 0 && (errno == EINVAL || errno == ERANGE)) return -2;
++p;
}
- kt_fisher_exact(d[0], d[1], d[2], d[3], &left, &right, &two);
- return is_single? right : two;
+ return test16_core(anno, a);
}
static void rm_info(int n_smpl, bcf1_t *b, const char *key)
static int update_bcf1(int n_smpl, bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr, double pref, int flag)
{
kstring_t s;
- int d[4], is_var = (pr->p_ref < pref);
- double p_hwe, p_dp, p_ed, r = is_var? pr->p_ref : 1. - pr->p_ref;
+ int is_var = (pr->p_ref < pref);
+ double p_hwe, r = is_var? pr->p_ref : 1. - pr->p_ref;
+ anno16_t a;
p_hwe = test_hwe(pr->g);
- p_ed = test_fisher(b, "ED4=", d, 1);
- p_dp = test_fisher(b, "DP4=", d, 0);
- rm_info(n_smpl, b, "ED4=");
+ test16(b, &a);
+ rm_info(n_smpl, b, "I16=");
memset(&s, 0, sizeof(kstring_t));
kputc('\0', &s); kputs(b->ref, &s); kputc('\0', &s);
kputs(b->info, &s);
if (b->info[0]) kputc(';', &s);
ksprintf(&s, "AF1=%.3lf;AFE=%.3lf", 1.-pr->f_em, 1.-pr->f_exp);
+ ksprintf(&s, ";DP4=%d,%d,%d,%d;MQ=%d", a.d[0], a.d[1], a.d[2], a.d[3], a.mq);
+ if (a.is_tested) ksprintf(&s, ";PV4=%.2lg,%.2lg,%.2lg,%.2lg", a.p[0], a.p[1], a.p[2], a.p[3]);
if (p_hwe <= .2) ksprintf(&s, ";GC=%.2lf,%.2lf,%.2lf;HWE=%.3lf", pr->g[2], pr->g[1], pr->g[0], p_hwe);
- if (p_dp >= 0. && p_dp <= .2) ksprintf(&s, ";TDP=%.3lf", p_dp);
- if (p_ed >= 0. && p_ed <= .2) ksprintf(&s, ";TED=%.3lf", p_ed);
kputc('\0', &s);
kputs(b->fmt, &s); kputc('\0', &s);
free(b->str);
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