void FastaIndex::readIndexFile(string fname) {
string line;
long long linenum = 0;
indexFile.open(fname.c_str(), ifstream::in);
if (indexFile.is_open()) {
while (getline (indexFile, line)) {
++linenum;
// the fai format defined in samtools is tab-delimited, every line being:
// fai->name[i], (int)x.len, (long long)x.offset, (int)x.line_blen, (int)x.line_len
vector<string> fields = split(line, '\t');
if (fields.size() == 5) { // if we don't get enough fields then there is a problem with the file
// note that fields[0] is the sequence name
char* end;
string name = split(fields[0], " \t").at(0); // key by first token of name
sequenceNames.push_back(name);
this->insert(make_pair(name, FastaIndexEntry(fields[0], atoi(fields[1].c_str()),
strtoll(fields[2].c_str(), &end, 10),
atoi(fields[3].c_str()),
atoi(fields[4].c_str()))));
} else {
cerr << "Warning: malformed fasta index file " << fname <<
"does not have enough fields @ line " << linenum << endl;
cerr << line << endl;
exit(1);
}
}
} else {
cerr << "could not open index file " << fname << endl;
exit(1);
}
}
void FastaIndex::flushEntryToIndex(FastaIndexEntry& entry) {
string name = split(entry.name, " \t").at(0); // key by first token of name
sequenceNames.push_back(name);
this->insert(make_pair(name, FastaIndexEntry(entry.name, entry.length,
entry.offset, entry.line_blen,
entry.line_len)));
}