void
get_ref_seq(const char* ref_seq_file,
std::string& ref_seq) {
static const unsigned buff_size(50000);
char buff[buff_size];
std::ifstream ref_is(ref_seq_file);
if ( ! ref_is ) {
log_os << "ERROR:: Can't open reference sequence file: " << ref_seq_file << "\n";
exit(EXIT_FAILURE);
}
#ifdef SEQ_UTIL_VERBOSE
log_os << "Reading from reference sequence file " << ref_seq_file << "\n";
#endif
ref_is.getline(buff,buff_size);
#ifdef SEQ_UTIL_VERBOSE
log_os << "First line: " << buff << "\n";
#endif
ref_seq.clear();
while (true) {
ref_is.getline(buff,buff_size);
if (! ref_is) {
if (ref_is.eof()) break;
else if (ref_is.fail()) {
if (ref_is.bad()) {
log_os << "ERROR:: unexpected failure while attempting to read sequence file: " << ref_seq_file << "\n";
exit(EXIT_FAILURE);
}
ref_is.clear();
}
}
ref_seq += buff;
}
#ifdef SEQ_UTIL_VERBOSE
log_os << "Finished reading from reference sequence file " << ref_seq_file << "\n";
log_os << "Reference sequence size: " << ref_seq.size() << "\n";
#endif
}
void
get_ref_seq(const char* ref_seq_file,
std::string& ref_seq,
const pos_range ref_segment)
{
static const unsigned buff_size(50000);
char buff[buff_size];
std::ifstream ref_is(ref_seq_file);
if ( ! ref_is )
{
log_os << "ERROR: Can't open reference sequence file: " << ref_seq_file << "\n";
exit(EXIT_FAILURE);
}
unsigned line_no(1);
#ifdef SEQ_UTIL_VERBOSE
log_os << "Reading from reference sequence file " << ref_seq_file << "\n";
#endif
ref_is.getline(buff,buff_size);
#ifdef SEQ_UTIL_VERBOSE
log_os << "First line: " << buff << "\n";
#endif
if (buff[0] != '>')
{
log_os << "ERROR: Unexpected format in reference sequence file: " << ref_seq_file << " line_no: " << line_no << "\n"
<< "\tline: '" << buff << "'\n";
exit(EXIT_FAILURE);
}
const pos_t begin_pos(ref_segment.is_begin_pos ? ref_segment.begin_pos : 0);
pos_t ref_pos(0);
ref_seq.clear();
while (true)
{
ref_is.getline(buff,buff_size);
if (! ref_is)
{
if (ref_is.eof()) break;
else if (ref_is.fail())
{
if (ref_is.bad())
{
log_os << "ERROR: unexpected failure while attempting to read sequence file: " << ref_seq_file << "\n";
exit(EXIT_FAILURE);
}
ref_is.clear();
}
}
line_no++;
if (buff[0] == '>')
{
log_os << "ERROR: Unexpected format in reference sequence file: " << ref_seq_file << " line_no: " << line_no << "\n"
<< "\tline: '" << buff << "'\n";
exit(EXIT_FAILURE);
}
// correct for '\r' if present:
pos_t rc(ref_is.gcount()-1);
if (rc && (buff[rc-1]=='\r'))
{
buff[--rc]='\0';
}
if (ref_segment.is_end_pos)
{
if (ref_pos>=ref_segment.end_pos) break;
if ((ref_pos+rc)>ref_segment.end_pos)
{
rc=(ref_segment.end_pos-ref_pos);
buff[rc]='\0';
}
}
if (ref_pos<begin_pos)
{
if ((ref_pos+rc) > begin_pos)
{
ref_seq += (buff+(begin_pos-ref_pos));
}
}
else
{
ref_seq += buff;
}
ref_pos += rc;
}
#ifdef SEQ_UTIL_VERBOSE
log_os << "Finished reading from reference sequence file " << ref_seq_file << "\n";
log_os << "Reference sequence size: " << ref_seq.size() << "\n";
#endif
}