Leandro Lima

This means requiring hits in a cluster to appear in the same order on a read as on a (single) path through the local graph. PS: when I read this...

Also tagged for debugging.

> For `QNAME` do you think it might be better to either add the specific region as either a pandora-specific tag, or alternatively it could be encoded in the CIGAR...

> In particular, `LF`, `RF` and `PPCH` are `pandora`-specific SAM extra fields, and can get quite large - I think we will by default remove these, but we can add...

> We could just take the [minimap2 approach](https://github.com/lh3/minimap2/issues/384) (I feel like I say that a lot ) and mark them, arbitrarily, as supplementary, but have the `tp:A` tag to designate...

With your suggestions, I inferred that the length of a PRG should be the length of its string representation (as `POS` is a position in this representation). This is required...

Yeah, I will take care of it after #23

Update: I am not taking care of this right after #23 This has low priority, moving towards finishing learning `pandora index, map and compare` to try to make the most...

This is a minor bug as it only affects the edges of the created `pandora.pangraph.gfa`, and it is only an "output" problem, i.e. the `pandora.pangraph.gfa` is indeed bugged, but it...

Hello @kdm9 , Thanks for the report! We can reproduce this on our end, as the `--clean` option is a bit unstable. We will deprecate it in the next minor...