inline bool get_intersect(const circle& a, const circle &b, bool e_trick, vector<node> &s) {
if (e_trick && a == b) {
add_interval(s, -PI, PI);
return true;
}
if (contain(a, b))
return false;
if (contain(b, a)) {
add_interval(s, -PI, PI);
return true;
}
point l = b.center - a.center;
double d = dis(a.center, b.center);
if (d > a.radius + b.radius - EPS)
return false;
double theta = acos((sqr(a.radius) + sqr(d) - sqr(b.radius)) / 2 / a.radius / d);
double c1 = atan2(l.y, l.x) - theta, c2 = atan2(l.y, l.x) + theta;
if (c1 < -PI) c1 += 2 * PI;
if (c2 > PI) c2 -= 2 * PI;
if (c1 > c2) {
add_interval(s, c1, PI);
add_interval(s, -PI, c2);
}
else
add_interval(s, c1, c2);
return true;
}
static int adjust_memory(struct pcmcia_socket *s, unsigned int action, unsigned long start, unsigned long end)
{
struct socket_data *data = s->resource_data;
unsigned long size = end - start + 1;
int ret = 0;
if (end < start)
return -EINVAL;
down(&rsrc_sem);
switch (action) {
case ADD_MANAGED_RESOURCE:
ret = add_interval(&data->mem_db, start, size);
break;
case REMOVE_MANAGED_RESOURCE:
ret = sub_interval(&data->mem_db, start, size);
if (!ret) {
struct pcmcia_socket *socket;
down_read(&pcmcia_socket_list_rwsem);
list_for_each_entry(socket, &pcmcia_socket_list, socket_list)
release_cis_mem(socket);
up_read(&pcmcia_socket_list_rwsem);
}
break;
default:
ret = -EINVAL;
}
up(&rsrc_sem);
return ret;
}
static int adjust_io(struct pcmcia_socket *s, unsigned int action, unsigned long start, unsigned long end)
{
struct socket_data *data = s->resource_data;
unsigned long size = end - start + 1;
int ret = 0;
if (end < start)
return -EINVAL;
if (end > IO_SPACE_LIMIT)
return -EINVAL;
down(&rsrc_sem);
switch (action) {
case ADD_MANAGED_RESOURCE:
if (add_interval(&data->io_db, start, size) != 0) {
ret = -EBUSY;
break;
}
#ifdef CONFIG_PCMCIA_PROBE
if (probe_io)
do_io_probe(s, start, size);
#endif
break;
case REMOVE_MANAGED_RESOURCE:
sub_interval(&data->io_db, start, size);
break;
default:
ret = -EINVAL;
break;
}
up(&rsrc_sem);
return ret;
}
inline vector<double> area(const vector<circle> &a) {
// return the area covered by at least x circlex
int n = a.size();
vector<double> ret(n + 1, 0);
for (int i = 0; i < n; ++i) {
vector<node> s;
int part = 0;
double last;
for (int j = 0; j < n; ++j)
get_intersect(a[i], a[j], i < j, s);
add_interval(s, -PI, PI);
sort(s.begin(), s.end(), cmp);
for (int j = 0; j < (int)s.size(); ++j) {
if (part)
ret[part] += calc_area(a[i], last, s[j].key);
part += s[j].value;
last = s[j].key;
}
}
return ret;
}
/**
* Constructor.
*
* @intervals - if empty, will add the contigs found in the header files
*/
BCFSyncedStreamReader::BCFSyncedStreamReader(std::vector<std::string>& vcf_files, std::vector<GenomeInterval>& intervals, bool sync_by_pos)
:vcf_files(vcf_files), intervals(intervals), sync_by_pos(sync_by_pos)
{
nfiles = vcf_files.size();
vcfs.resize(nfiles, 0);
hdrs.resize(nfiles, 0);
idxs.resize(nfiles, 0);
tbxs.resize(nfiles, 0);
itrs.resize(nfiles, 0);
ftypes.resize(nfiles, -1);
current_interval = "";
current_pos1 = 0;
buffer.resize(nfiles);
s = {0, 0, 0};
exists_selected_intervals = (intervals.size()!=0);
for (uint32_t i=0; i<intervals.size(); ++i)
{
intervals_map[intervals[i].to_string()] = i;
}
intervals_index = 0;
//1. check file type validity
//2. loads indices
//3. adds sequences found in all indexed files, this allows us to iterate through all sequences.
for (int32_t i = 0; i<nfiles; ++i)
{
ftypes[i] = hts_file_type(vcf_files[i].c_str());
vcfs[i] = bcf_open(vcf_files[i].c_str(), "r");
if (vcfs[i]==NULL) exit(1);
hdrs[i] = bcf_alt_hdr_read(vcfs[i]);
if (i==0)
{
if (!(ftypes[i] & (FT_VCF|FT_BCF|FT_STDIN)))
{
fprintf(stderr, "[E:%s:%d %s] %s not a VCF or BCF file\n", __FILE__, __LINE__, __FUNCTION__, vcf_files[i].c_str());
exit(1);
}
if (!load_index(i))
{
fprintf(stderr, "[I:%s:%d %s] index cannot be loaded for %s\n", __FILE__, __LINE__, __FUNCTION__, vcf_files[i].c_str());
exit(1);
}
if (!exists_selected_intervals)
{
//add sequences from file i
add_interval(i);
}
}
else
{
if (!(ftypes[i] & (FT_VCF_GZ|FT_BCF_GZ)))
{
fprintf(stderr, "[E:%s:%d %s] %s not a VCF_GZ or BCF file\n", __FILE__, __LINE__, __FUNCTION__, vcf_files[i].c_str());
exit(1);
}
if (!load_index(i))
{
fprintf(stderr, "[E:%s:%d %s] index cannot be loaded for %s\n", __FILE__, __LINE__, __FUNCTION__, vcf_files[i].c_str());
exit(1);
}
if (!exists_selected_intervals)
{
//add sequences from file i
add_interval(i);
}
}
}
}
