bool GenomicRegionCollection<T>::ReadVCF(const std::string & file, const BamHeader& hdr) {
m_sorted = false;
idx = 0;
gzFile fp = NULL;
fp = strcmp(file.c_str(), "-")? gzopen(file.c_str(), "r") : gzdopen(fileno(stdin), "r");
if (file.empty() || !fp) {
std::cerr << "VCF file not readable: " << file << std::endl;
return false;
}
// http://www.lemoda.net/c/gzfile-read/
while (1) {
int err;
char buffer[GZBUFFER];
gzgets(fp, buffer, GZBUFFER);
int bytes_read = strlen(buffer);
// get one line
if (bytes_read < GZBUFFER - 1) {
if (gzeof (fp)) break;
else {
const char * error_string;
error_string = gzerror (fp, &err);
if (err) {
fprintf (stderr, "Error: %s.\n", error_string);
exit (EXIT_FAILURE);
}
}
}
// prepare to loop through each field of BED line
std::string chr, pos;
std::string line(buffer);
std::istringstream iss_line(line);
std::string val;
if (line.empty() || line.at(0) == '#')
continue;
// read first two columnes
iss_line >> chr >> pos;
// construct the GenomicRegion
T gr;
try {
gr = T(chr, pos, pos, hdr);
} catch (...) {
std::cerr << "...Could not parse pos: " << pos << std::endl << std::endl
<< "...on line " << line << std::endl;
}
if (gr.chr >= 0)
m_grv->push_back(gr);
}
return true;
}
bool GenomicRegionCollection<T>::ReadBED(const std::string & file, const BamHeader& hdr) {
m_sorted = false;
idx = 0;
gzFile fp = NULL;
fp = strcmp(file.c_str(), "-")? gzopen(file.c_str(), "r") : gzdopen(fileno(stdin), "r");
if (file.empty() || !fp) {
std::cerr << "BED file not readable: " << file << std::endl;
return false;
}
// http://www.lemoda.net/c/gzfile-read/
while (1) {
int err;
char buffer[GZBUFFER];
gzgets(fp, buffer, GZBUFFER);
int bytes_read = strlen(buffer);
// get one line
if (bytes_read < GZBUFFER - 1) {
if (gzeof (fp)) break;
else {
const char * error_string;
error_string = gzerror (fp, &err);
if (err) {
fprintf (stderr, "Error: %s.\n", error_string);
exit (EXIT_FAILURE);
}
}
}
// prepare to loop through each field of BED line
//size_t counter = 0;
std::string chr, pos1, pos2;
std::string line(buffer);
std::istringstream iss_line(line);
std::string val;
if (line.find("#") != std::string::npos)
continue;
// read first three BED columns
iss_line >> chr >> pos1 >> pos2;
// construct the GenomicRegion
T gr(chr, pos1, pos2, hdr);
if (gr.chr >= 0)
m_grv->push_back(gr);
}
return true;
}
name_value_pairs::name_value_pairs(std::string const& filename)
{
std::ifstream is(filename.c_str());
std::string line;
while(std::getline(is, line))
{
std::istringstream iss_line(line);
if(std::string::npos == line.find_first_of('='))
{
continue;
}
std::string name;
std::getline(iss_line, name, '=');
std::string value;
std::getline(iss_line, value);
map_[name] = value;
}
}
/**
* \brief Initialise the item.
*/
void bear::rolling_credits::build()
{
super::build();
std::stringstream iss;
engine::resource_pool::get_instance().get_file(m_file, iss);
if ( m_fading_frac < 0 )
m_fading_frac = 1.0 / 4;
else
// initially, m_fading_frac contains the duration of the fading
m_fading_frac /= m_movement_duration;
std::string line;
visual::font font;
double font_size(12);
double red(1), green(1), blue(1), opacity(1);
visual::text_align::horizontal_align horizontal_align
( visual::text_align::align_center );
visual::size_type width( get_width() );
while ( claw::text::getline(iss, line) )
if ( line.empty() )
m_lines.push_back
( credit_line
( line, font, red, green, blue, opacity, get_bottom_left(), width,
horizontal_align ) );
else if ( line[0] == '#' )
{
std::string s;
std::istringstream iss_line(line);
iss_line >> s;
if ( s == "#color" )
{
red = green = blue = opacity = 1;
iss_line >> red >> green >> blue >> opacity;
}
