void
standardize_ref_seq(const char* ref_seq_file,
const char* chr_name,
std::string& ref_seq,
const pos_t offset)
{
const std::string::size_type ref_size(ref_seq.size());
for (std::string::size_type i(0); i<ref_size; ++i)
{
const char old_ref(ref_seq[i]);
char c(old_ref);
if (islower(c)) c = toupper(c);
if (! is_valid_base(c))
{
if (! is_iupac_base(c))
{
static const char def_chr_name[] = "first-sequence-in-file";
const char* seq_name(NULL != chr_name ? chr_name : def_chr_name);
log_os << "ERROR:: Unexpected character in reference sequence.\n";
log_os << "\treference_sequence_file: '" << ref_seq_file << "'\n";
log_os << "\tchromosome: '" << seq_name << "'\n";
log_os << "\tcharacter: '" << old_ref << "'\n";
log_os << "\tcharacter_decimal_index: " << static_cast<int>(old_ref) << "\n";
log_os << "\tcharacter_position_in_chromosome: " << (i+1+offset) << "\n";
exit(EXIT_FAILURE);
}
c=elandize_base(c);
}
if (c != old_ref) ref_seq[i] = c;
}
}
void
standardize_ref_seq(const char* ref_seq_file,
std::string& ref_seq) {
const std::string::size_type ref_size(ref_seq.size());
for (std::string::size_type i(0); i<ref_size; ++i) {
const char old_ref(ref_seq[i]);
char c(old_ref);
if (islower(c)) c = toupper(c);
if (! is_valid_base(c)) {
if (! is_iupac_base(c)) {
log_os << "ERROR:: Unexpected character in reference sequence.\n";
log_os << "\treference-sequence: " << ref_seq_file << "\n";
log_os << "\tcharacter: '" << old_ref << "'\n";
log_os << "\tcharacter-position: " << (i+1) << "\n";
exit(EXIT_FAILURE);
}
c=elandize_base(c);
}
if (c != old_ref) ref_seq[i] = c;
}
}
