Delly with empty BED file

[fgvieira]

Dear all,

running delly with an empty BED gives an error:

Exclude file is missing: [...]

Would it be possible to, when BED file is empty, to just ignore it and print a warning? I think it would be just a matter of tweaking these lines: https://github.com/dellytools/delly/blob/cace738093348cb8b1c12b26a83d527c0a92c667/src/delly.h#L340-L346

thanks,

[tobiasrausch]

The BED file is not a mandatory option. If it is empty you shouldn't specify it on the command-line.

[fgvieira]

yes, but when running delly through a pipeline, you not always know if the BED file will be empty or not (since delly requires the complement). Another way would be to also allow for a BED with regions to include (rather than only exclude).

[fgvieira]

Hi @tobiasrausch,

I see that you just released a new version of delly, would it be possible to also have an include BED file option (like, e.g., in manta or other SV callers)? It would be a great help for me. :smile:

thanks in advance for your help.