triangle: -E output order change
Brian Ondov
4 years ago
| 34 | 34 | useOption("help"); |
| 35 | 35 | addOption("list", Option(Option::Boolean, "l", "Input", "List input. Lines in each <query> specify paths to sequence files, one per line. The reference file is not affected.", "")); |
| 36 | 36 | addOption("comment", Option(Option::Boolean, "C", "Output", "Use comment fields for sequence names instead of IDs.", "")); |
| 37 | addOption("edge", Option(Option::Boolean, "E", "Output", "Output edge list with fields [seq1, seq2, dist, p-val, shared-hashes].", "")); | |
| 37 | addOption("edge", Option(Option::Boolean, "E", "Output", "Output edge list instead of Phylip matrix, with fields [seq1, seq2, dist, p-val, shared-hashes].", "")); | |
| 38 | 38 | //addOption("log", Option(Option::Boolean, "L", "Output", "Log scale distances and divide by k-mer size to provide a better analog to phylogenetic distance. The special case of zero shared min-hashes will result in a distance of 1.", "")); |
| 39 | 39 | useSketchOptions(); |
| 40 | 40 | } |
| 163 | 163 | if ( edge ) |
| 164 | 164 | { |
| 165 | 165 | const Sketch::Reference & qry = sketch.getReference(i); |
| 166 | cout << (comment ? qry.comment : qry.name) << '\t'<< (comment ? ref.comment : ref.name) << '\t' << pair->distance << endl;// << '\t' << pair->pValue << '\t' << pair->numer << '/' << pair->denom << endl; | |
| 166 | cout << (comment ? ref.comment : ref.name) << '\t'<< (comment ? qry.comment : qry.name) << '\t' << pair->distance << endl;// << '\t' << pair->pValue << '\t' << pair->numer << '/' << pair->denom << endl; | |
| 167 | 167 | } |
| 168 | 168 | else |
| 169 | 169 | { |