#include "bam.h"
#include "bam_maqcns.h"
#include "ksort.h"
+#include "errmod.h"
#include "kaln.h"
KSORT_INIT_GENERIC(uint32_t)
typedef struct __bmc_aux_t {
int max;
uint32_t *info;
+ uint16_t *info16;
+ errmod_t *em;
} bmc_aux_t;
typedef struct {
float esum[4], fsum[4];
uint32_t c[4];
- uint32_t rms_mapQ;
} glf_call_aux_t;
char bam_nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };
for (n1 = 0; n1 < 256; ++n1) {
for (n2 = 0; n2 < 256; ++n2) {
long double sum = 0.0;
- double lC = aa->is_soap? 0 : lgamma(n1+n2+1) - lgamma(n1+1) - lgamma(n2+1); // \binom{n1+n2}{n1}
+ double lC = aa->errmod == BAM_ERRMOD_SOAP? 0 : lgamma(n1+n2+1) - lgamma(n1+1) - lgamma(n2+1);
for (k = 1; k <= aa->n_hap - 1; ++k) {
double pk = 1.0 / k / sum_harmo;
double log1 = log((double)k/aa->n_hap);
long double sum_a[257], b[256], q_c[256], tmp[256], fk2[256];
double *lC;
+ if (aa->errmod == BAM_ERRMOD_MAQ2) return; // no need to do the following
// aa->lhet will be allocated and initialized
free(aa->fk); free(aa->coef);
aa->coef = 0;
aa->fk[n] = pow(aa->theta, n) * (1.0 - aa->eta) + aa->eta;
fk2[n] = aa->fk[n>>1]; // this is an approximation, assuming reads equally likely come from both strands
}
- if (aa->is_soap) return;
+ if (aa->errmod == BAM_ERRMOD_SOAP) return;
aa->coef = (double*)calloc(256*256*64, sizeof(double));
lC = (double*)calloc(256 * 256, sizeof(double));
for (n = 1; n != 256; ++n)
bm = (bam_maqcns_t*)calloc(1, sizeof(bam_maqcns_t));
bm->aux = (bmc_aux_t*)calloc(1, sizeof(bmc_aux_t));
bm->het_rate = 0.001;
- bm->theta = 0.85;
+ bm->theta = 0.83f;
bm->n_hap = 2;
bm->eta = 0.03;
bm->cap_mapQ = 60;
+ bm->min_baseQ = 13;
return bm;
}
void bam_maqcns_prepare(bam_maqcns_t *bm)
{
+ if (bm->errmod == BAM_ERRMOD_MAQ2) bm->aux->em = errmod_init(1. - bm->theta);
cal_coef(bm); cal_het(bm);
}
void bam_maqcns_destroy(bam_maqcns_t *bm)
{
if (bm == 0) return;
- free(bm->lhet); free(bm->fk); free(bm->coef); free(bm->aux->info);
+ free(bm->lhet); free(bm->fk); free(bm->coef); free(bm->aux->info); free(bm->aux->info16);
+ if (bm->aux->em) errmod_destroy(bm->aux->em);
free(bm->aux); free(bm);
}
glf1_t *bam_maqcns_glfgen(int _n, const bam_pileup1_t *pl, uint8_t ref_base, bam_maqcns_t *bm)
{
- glf_call_aux_t *b;
+ glf_call_aux_t *b = 0;
int i, j, k, w[8], c, n;
glf1_t *g = (glf1_t*)calloc(1, sizeof(glf1_t));
float p[16], min_p = 1e30;
bm->aux->max = _n;
kroundup32(bm->aux->max);
bm->aux->info = (uint32_t*)realloc(bm->aux->info, 4 * bm->aux->max);
+ bm->aux->info16 = (uint16_t*)realloc(bm->aux->info16, 2 * bm->aux->max);
}
- for (i = n = 0; i < _n; ++i) {
+ for (i = n = 0, rms = 0; i < _n; ++i) {
const bam_pileup1_t *p = pl + i;
uint32_t q, x = 0, qq;
+ uint16_t y = 0;
if (p->is_del || (p->b->core.flag&BAM_FUNMAP)) continue;
q = (uint32_t)bam1_qual(p->b)[p->qpos];
+ if (q < bm->min_baseQ) continue;
x |= (uint32_t)bam1_strand(p->b) << 18 | q << 8 | p->b->core.qual;
+ y |= bam1_strand(p->b)<<4;
if (p->b->core.qual < q) q = p->b->core.qual;
+ c = p->b->core.qual < bm->cap_mapQ? p->b->core.qual : bm->cap_mapQ;
+ rms += c * c;
x |= q << 24;
+ y |= q << 5;
qq = bam1_seqi(bam1_seq(p->b), p->qpos);
q = bam_nt16_nt4_table[qq? qq : ref_base];
- if (!p->is_del && q < 4) x |= 1 << 21 | q << 16;
+ if (!p->is_del && q < 4) x |= 1 << 21 | q << 16, y |= q;
+ bm->aux->info16[n] = y;
bm->aux->info[n++] = x;
}
+ rms = (uint8_t)(sqrt((double)rms / n) + .499);
+ if (bm->errmod == BAM_ERRMOD_MAQ2) {
+ errmod_cal(bm->aux->em, n, 4, bm->aux->info16, p);
+ goto goto_glf;
+ }
ks_introsort(uint32_t, n, bm->aux->info);
// generate esum and fsum
b = (glf_call_aux_t*)calloc(1, sizeof(glf_call_aux_t));
for (k = 0; k != 8; ++k) w[k] = 0;
- rms = 0;
for (j = n - 1; j >= 0; --j) { // calculate esum and fsum
uint32_t info = bm->aux->info[j];
- int tmp;
if (info>>24 < 4 && (info>>8&0x3f) != 0) info = 4<<24 | (info&0xffffff);
k = info>>16&7;
if (info>>24 > 0) {
if (w[k] < 0xff) ++w[k];
++b->c[k&3];
}
- tmp = (int)(info&0xff) < bm->cap_mapQ? (int)(info&0xff) : bm->cap_mapQ;
- rms += tmp * tmp;
}
- b->rms_mapQ = (uint8_t)(sqrt((double)rms / n) + .499);
// rescale ->c[]
for (j = c = 0; j != 4; ++j) c += b->c[j];
if (c > 255) {
for (j = 0; j != 4; ++j) b->c[j] = (int)(254.0 * b->c[j] / c + 0.5);
for (j = c = 0; j != 4; ++j) c += b->c[j];
}
- if (!bm->is_soap) {
+ if (bm->errmod == BAM_ERRMOD_MAQ) {
// generate likelihood
for (j = 0; j != 4; ++j) {
// homozygous
if (max1 > max2 && (min_k != max_k || min1 + 1.0 > min2))
p[max_k<<2|max_k] = min1 > 1.0? min1 - 1.0 : 0.0;
}
- } else { // apply the SOAP model
+ } else if (bm->errmod == BAM_ERRMOD_SOAP) { // apply the SOAP model
// generate likelihood
for (j = 0; j != 4; ++j) {
float tmp;
}
}
+goto_glf:
// convert necessary information to glf1_t
- g->ref_base = ref_base; g->max_mapQ = b->rms_mapQ;
+ g->ref_base = ref_base; g->max_mapQ = rms;
g->depth = n > 16777215? 16777215 : n;
for (j = 0; j != 4; ++j)
for (k = j; k < 4; ++k)
uint32_t glf2cns(const glf1_t *g, int q_r)
{
- int i, j, k, tmp[16], min = 10000, min2 = 10000, min3 = 10000, min_g = -1, min_g2 = -1;
+ int i, j, k, p[10], ref4;
uint32_t x = 0;
+ ref4 = bam_nt16_nt4_table[g->ref_base];
for (i = k = 0; i < 4; ++i)
for (j = i; j < 4; ++j) {
- tmp[j<<2|i] = -1;
- tmp[i<<2|j] = g->lk[k++] + (i == j? 0 : q_r);
+ int prior = (i == ref4 && j == ref4? 0 : i == ref4 || j == ref4? q_r : q_r + 3);
+ p[k] = (g->lk[k] + prior)<<4 | i<<2 | j;
+ ++k;
}
- for (i = 0; i < 16; ++i) {
- if (tmp[i] < 0) continue;
- if (tmp[i] < min) {
- min3 = min2; min2 = min; min = tmp[i]; min_g2 = min_g; min_g = i;
- } else if (tmp[i] < min2) {
- min3 = min2; min2 = tmp[i]; min_g2 = i;
- } else if (tmp[i] < min3) min3 = tmp[i];
- }
- x = min_g >= 0? (1U<<(min_g>>2&3) | 1U<<(min_g&3)) << 28 : 0xf << 28;
- x |= min_g2 >= 0? (1U<<(min_g2>>2&3) | 1U<<(min_g2&3)) << 24 : 0xf << 24;
- x |= (uint32_t)g->max_mapQ << 16;
- x |= min2 < 10000? (min2 - min < 256? min2 - min : 255) << 8 : 0xff << 8;
- x |= min2 < 10000 && min3 < 10000? (min3 - min2 < 256? min3 - min2 : 255) : 0xff;
+ for (i = 1; i < 10; ++i) // insertion sort
+ for (j = i; j > 0 && p[j] < p[j-1]; --j)
+ k = p[j], p[j] = p[j-1], p[j-1] = k;
+ x = (1u<<(p[0]&3) | 1u<<(p[0]>>2&3)) << 28; // the best genotype
+ x |= (uint32_t)g->max_mapQ << 16; // rms mapQ
+ x |= ((p[1]>>4) - (p[0]>>4) < 256? (p[1]>>4) - (p[0]>>4) : 255) << 8; // consensus Q
+ for (k = 0; k < 10; ++k)
+ if ((p[k]&0xf) == (ref4<<2|ref4)) break;
+ if (k == 10) k = 9;
+ x |= (p[k]>>4) - (p[0]>>4) < 256? (p[k]>>4) - (p[0]>>4) : 255; // snp Q
return x;
}
uint32_t x;
if (n) {
g = bam_maqcns_glfgen(n, pl, 0xf, bm);
- x = glf2cns(g, (int)(bm->q_r + 0.5));
+ x = g->depth == 0? (0xfU<<28 | 0xfU<<24) : glf2cns(g, (int)(bm->q_r + 0.5));
free(g);
} else x = 0xfU<<28 | 0xfU<<24;
return x;
for (i = 0; i < n_types; ++i) {
ka_param_t ap = ka_param_blast;
ap.band_width = 2 * types[n_types - 1] + 2;
- ap.gap_end = 0;
+ ap.gap_end_ext = 0;
// write ref2
for (k = 0, j = left; j <= pos; ++j)
ref2[k++] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[j]]];
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