Exemple #1
0
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);
}
Exemple #2
0
// 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;
}
Exemple #3
0
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;
}