bigtools bedgraphtobigwig -- add option to skip invalid chromosomes

[nleroy917]

wigToBigWig has an option -clip to simply issue a warning instead of crashing when a chromosome not represented in chrom.sizes file is found in the .wig file:

-clip - If set just issue warning messages rather than dying if wig
                  file contains items off end of chromosome or chromosomes
                  that are not in the chrom.sizes file.

Is it possible to have similar functionality in bedgraphtobigwig? I would imagine a similar flag like --clip

[jackh726]

Seems simple enough :) I'll add this over the weekend.

[nleroy917]

Thanks a lot! I’d love to take a crack at it, since I’m currently learning Rust.. hadn't gotten a chance to dive too deeply, though.

[jackh726]

Please feel free :) Very happy to answer questions or guide you if you need!

[jackh726]

@nleroy917 are you still interested in this?

[nleroy917]

Yes! Sorry I wasnt able to get to it this weekend, but this week I should! Unless you are in a hurry to close the issue which is understandable!

[jackh726]

No, you are more than welcome to it :) no rush from me