# ograph¶

ograph finds the overlap graph of one or more pqueries.

```
usage: ograph [options] placefile
```

## Options¶

-o |
Specify the filename to write to. |

--out-dir |
Specify the directory to write files to. |

--prefix |
Specify a string to be prepended to filenames. |

--pp |
Use posterior probability for the weight. |

## Details¶

The overlap of a pair of pqueries is defined to be the inner product of their likelihood weight ratios (or posterior probabilities) as indexed by tree edges.

This subcommand outputs all nonzero overlaps between pqueries in the form:

```
pquery_1 pquery_2 inner_product
```

which is a specification of the weighted edges of a graph with pqueries as vertices.