| 176 | }; |
| 177 | |
| 178 | void |
| 179 | check_options(int argc, bool& die) |
| 180 | { |
| 181 | if (opt::bloomSize == 0) { |
| 182 | std::cerr << PROGRAM ": missing or invalid value for mandatory option `-b'" << std::endl; |
| 183 | die = true; |
| 184 | } |
| 185 | |
| 186 | if (argc - optind < 3) { |
| 187 | std::cerr << PROGRAM ": missing input file arguments" << std::endl; |
| 188 | die = true; |
| 189 | } |
| 190 | |
| 191 | if (opt::k <= 0) { |
| 192 | std::cerr << PROGRAM ": missing or invalid value for mandatory option `-k'" << std::endl; |
| 193 | die = true; |
| 194 | } |
| 195 | |
| 196 | if (opt::readQualityThreshold <= 0) { |
| 197 | std::cerr << PROGRAM ": invalid value for option `-q'" << std::endl; |
| 198 | die = true; |
| 199 | } |
| 200 | |
| 201 | if (opt::outputGraphPath.empty()) { |
| 202 | std::cerr << PROGRAM ": missing or invalid value for mandatory option `-g`" << std::endl; |
| 203 | die = true; |
| 204 | } |
| 205 | |
| 206 | if (opt::outputContigsPath.empty()) { |
| 207 | std::cerr << PROGRAM ": missing or invalid value for mandatory option `-c`" << std::endl; |
| 208 | die = true; |
| 209 | } |
| 210 | |
| 211 | if (opt::threads <= 0) { |
| 212 | std::cerr << PROGRAM ": invalid number of threads `-j`" << std::endl; |
| 213 | die = true; |
| 214 | } |
| 215 | |
| 216 | if (opt::minTests > opt::maxTests) { |
| 217 | std::cerr << PROGRAM ": --min-tests cannot be higher than --max-tests" << std::endl; |
| 218 | die = true; |
| 219 | } |
| 220 | } |
| 221 | |
| 222 | void |
| 223 | writePaths(std::ostream& stream, const ImaginaryContigPaths& paths) |