void bcf_remove_alleles(const bcf_hdr_t *header, bcf1_t *line, int rm_mask)
{
int i;
kbitset_t *rm_set = kbs_init(line->n_allele);
for (i=1; i<line->n_allele; i++)
if ( rm_mask & 1<<i ) kbs_insert(rm_set, i);
bcf_remove_allele_set(header, line, rm_set);
kbs_destroy(rm_set);
}
// Resize a bit set.
static inline kbitset_t *kbs_resize(kbitset_t *bs, size_t ni)
{
if ( !bs ) return kbs_init(ni);
size_t n = (ni + KBS_ELTBITS-1) / KBS_ELTBITS;
if ( n==bs->n ) return bs;
bs = (kbitset_t *) realloc(bs, sizeof(kbitset_t) + n * sizeof(unsigned long));
if ( bs==NULL ) return NULL;
if ( n > bs->n )
memset(bs->b + bs->n, 0, (n - bs->n) * sizeof (unsigned long));
bs->n = n;
bs->b[n] = ~0UL;
return bs;
}
int bcf_trim_alleles(const bcf_hdr_t *header, bcf1_t *line)
{
int i;
bcf_fmt_t *gt = bcf_get_fmt(header, line, "GT");
if ( !gt ) return 0;
int *ac = (int*) calloc(line->n_allele,sizeof(int));
// check if all alleles are populated
#define BRANCH(type_t,vector_end) { \
for (i=0; i<line->n_sample; i++) \
{ \
type_t *p = (type_t*) (gt->p + i*gt->size); \
int ial; \
for (ial=0; ial<gt->n; ial++) \
{ \
if ( p[ial]==vector_end ) break; /* smaller ploidy */ \
if ( bcf_gt_is_missing(p[ial]) ) continue; /* missing allele */ \
if ( (p[ial]>>1)-1 >= line->n_allele ) { free(ac); return -1; } \
ac[(p[ial]>>1)-1]++; \
} \
} \
}
switch (gt->type) {
case BCF_BT_INT8: BRANCH(int8_t, bcf_int8_vector_end); break;
case BCF_BT_INT16: BRANCH(int16_t, bcf_int16_vector_end); break;
case BCF_BT_INT32: BRANCH(int32_t, bcf_int32_vector_end); break;
default: fprintf(stderr, "[E::%s] todo: %d at %s:%d\n", __func__, gt->type, header->id[BCF_DT_CTG][line->rid].key, line->pos+1); exit(1); break;
}
#undef BRANCH
int nrm = 0;
kbitset_t *rm_set = kbs_init(line->n_allele);
for (i=1; i<line->n_allele; i++)
{
if ( !ac[i] ) { kbs_insert(rm_set, i); nrm++; }
}
free(ac);
if ( nrm ) bcf_remove_allele_set(header, line, rm_set);
kbs_destroy(rm_set);
return nrm;
}
