# psltools score
PSL has no score column, so `score` is a reporting / sort-key tool. It prints
`queryName<TAB>referenceName<TAB>value` for a chosen metric.
```
psltools score [-c "IN.psl ..."] [-o OUT.tsv] [--metric M] [--mrna] [--sort-by-score] [-G]
```
| `--metric` | `score` | `score` (`pslScore`), `milli-bad`, or `percent-id`. |
| `--mrna` | off | Treat alignments as mRNA (affects `milli-bad`/`percent-id`).|
| `--sort-by-score` | off | Emit rows ordered by computed `pslScore`, descending. |
| `-G, --gzip` | off | Compress output. |
All metrics reproduce UCSC `kent/src/lib/psl.c` integer semantics exactly; the
protein `sizeMul` is derived per record.
```bash
psltools score -c in.psl --metric percent-id --mrna