Exemplo n.º 1
0
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);
    }
}
Exemplo n.º 2
0
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)));

}