if (theta <= 0.) theta = CALL_DEFTHETA;
bca = calloc(1, sizeof(bcf_callaux_t));
bca->capQ = 60;
if (theta <= 0.) theta = CALL_DEFTHETA;
bca = calloc(1, sizeof(bcf_callaux_t));
bca->capQ = 60;
* negative if we are looking at an indel. */
int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r)
{
* negative if we are looking at an indel. */
int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r)
{
- int i, n, ref4, is_indel;
+ int i, n, ref4, is_indel, ori_depth = 0;
memset(r, 0, sizeof(bcf_callret1_t));
if (ref_base >= 0) {
ref4 = bam_nt16_nt4_table[ref_base];
memset(r, 0, sizeof(bcf_callret1_t));
if (ref_base >= 0) {
ref4 = bam_nt16_nt4_table[ref_base];
memset(r, 0, sizeof(bcf_callret1_t));
for (i = n = 0; i < _n; ++i) {
const bam_pileup1_t *p = pl + 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, baseQ, is_diff, min_dist;
+ int q, b, mapQ, baseQ, is_diff, min_dist, seqQ;
- mapQ = p->b->core.qual < bca->capQ? p->b->core.qual : bca->capQ;
+ if (q > seqQ) q = seqQ;
+ mapQ = p->b->core.qual < 255? p->b->core.qual : DEF_MAPQ; // special case for mapQ==255
+ mapQ = mapQ < bca->capQ? mapQ : bca->capQ;
b = bam_nt16_nt4_table[b? b : ref_base]; // b is the 2-bit base
is_diff = (ref4 < 4 && b == ref4)? 0 : 1;
} else {
b = bam_nt16_nt4_table[b? b : ref_base]; // b is the 2-bit base
is_diff = (ref4 < 4 && b == ref4)? 0 : 1;
} else {
++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;
++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;
// glfgen
errmod_cal(bca->e, n, 5, bca->bases, r->p);
return r->depth;
// glfgen
errmod_cal(bca->e, n, 5, bca->bases, r->p);
return r->depth;
if (((ref4 < 4 && j < 4) || (ref4 == 4 && j < 5)) && i >= 0)
call->unseen = j, call->a[j++] = qsum[i]&3;
call->n_alleles = j;
if (((ref4 < 4 && j < 4) || (ref4 == 4 && j < 5)) && i >= 0)
call->unseen = j, call->a[j++] = qsum[i]&3;
call->n_alleles = j;
x = call->n_alleles * (call->n_alleles + 1) / 2;
// get the possible genotypes
for (i = z = 0; i < call->n_alleles; ++i)
x = call->n_alleles * (call->n_alleles + 1) / 2;
// get the possible genotypes
for (i = z = 0; i < call->n_alleles; ++i)
for (i = 0; i < n; ++i) {
uint8_t *PL = call->PL + x * i;
const bcf_callret1_t *r = calls + i;
for (i = 0; i < n; ++i) {
uint8_t *PL = call->PL + x * i;
const bcf_callret1_t *r = calls + i;
if (bca->indel_types[bc->a[i]] < 0) { // deletion
for (j = -bca->indel_types[bc->a[i]]; j < bca->indelreg; ++j)
kputc(ref[pos+1+j], &s);
if (bca->indel_types[bc->a[i]] < 0) { // deletion
for (j = -bca->indel_types[bc->a[i]]; j < bca->indelreg; ++j)
kputc(ref[pos+1+j], &s);
memcpy(b->gi[0].data, bc->PL, b->gi[0].len * bc->n);
if (bcr) {
uint16_t *dp = (uint16_t*)b->gi[1].data;
memcpy(b->gi[0].data, bc->PL, b->gi[0].len * bc->n);
if (bcr) {
uint16_t *dp = (uint16_t*)b->gi[1].data;
for (i = 0; i < bc->n; ++i) {
bcf_callret1_t *p = bcr + i;
dp[i] = p->depth < 0xffff? p->depth : 0xffff;
for (i = 0; i < bc->n; ++i) {
bcf_callret1_t *p = bcr + i;
dp[i] = p->depth < 0xffff? p->depth : 0xffff;