unsigned int
#elif ULONG_MAX == 0xffffffffu
unsigned long
#endif
bgpstream_ipv4_pfx_hash(bgpstream_ipv4_pfx_t *pfx)
{
// embed the network mask length in the 32 bits
return __ac_Wang_hash(pfx->address.ipv4.s_addr | (uint32_t)pfx->mask_len);
}
unsigned long
#else
unsigned long long
#endif
bgpstream_ipv6_pfx_hash(bgpstream_ipv6_pfx_t *pfx)
{
// ipv6 number - we take most significant 64 bits only
unsigned char *s6 = &(pfx->address.ipv6.s6_addr[0]);
uint64_t address = *((uint64_t *) s6);
// embed the network mask length in the 64 bits
return __ac_Wang_hash(address | (uint64_t)pfx->mask_len);
}
// Returns 0 to indicate read should be output 1 otherwise
static int process_aln(const bam_hdr_t *h, bam1_t *b, samview_settings_t* settings)
{
if (settings->remove_B) bam_remove_B(b);
if (settings->min_qlen > 0) {
int k, qlen = 0;
uint32_t *cigar = bam_get_cigar(b);
for (k = 0; k < b->core.n_cigar; ++k)
if ((bam_cigar_type(bam_cigar_op(cigar[k]))&1) || bam_cigar_op(cigar[k]) == BAM_CHARD_CLIP)
qlen += bam_cigar_oplen(cigar[k]);
if (qlen < settings->min_qlen) return 1;
}
if (b->core.qual < settings->min_mapQ || ((b->core.flag & settings->flag_on) != settings->flag_on) || (b->core.flag & settings->flag_off))
return 1;
if (settings->bed && (b->core.tid < 0 || !bed_overlap(settings->bed, h->target_name[b->core.tid], b->core.pos, bam_endpos(b))))
return 1;
if (settings->subsam_frac > 0.) {
uint32_t k = __ac_Wang_hash(__ac_X31_hash_string(bam_get_qname(b)) ^ settings->subsam_seed);
if ((double)(k&0xffffff) / 0x1000000 >= settings->subsam_frac) return 1;
}
if (settings->rghash) {
uint8_t *s = bam_aux_get(b, "RG");
if (s) {
khint_t k = kh_get(rg, settings->rghash, (char*)(s + 1));
if (k == kh_end(settings->rghash)) return 1;
}
}
if (settings->library) {
const char *p = bam_get_library((bam_hdr_t*)h, b);
if (!p || strcmp(p, settings->library) != 0) return 1;
}
if (settings->remove_aux_len) {
size_t i;
for (i = 0; i < settings->remove_aux_len; ++i) {
uint8_t *s = bam_aux_get(b, settings->remove_aux[i]);
if (s) {
bam_aux_del(b, s);
}
}
}
return 0;
}
