Align multiple sequences. */
| 108 | |
| 109 | /** Align multiple sequences. */ |
| 110 | static void alignFile(const char* path) { |
| 111 | if (opt::verbose > 0) |
| 112 | cerr << "Aligning `" << path << "'\n"; |
| 113 | FastaReader in(path, FastaReader::NO_FOLD_CASE); |
| 114 | for (vector<string> seq; in;) { |
| 115 | seq.clear(); |
| 116 | FastaRecord fa; |
| 117 | if (in >> fa) |
| 118 | seq.push_back(fa.seq); |
| 119 | while (in.peek() == '>' && in >> fa) |
| 120 | seq.push_back(fa.seq); |
| 121 | align(seq, cout); |
| 122 | } |
| 123 | assert(in.eof()); |
| 124 | } |
| 125 | |
| 126 | int main(int argc, char** argv) |
| 127 | { |