Add -B for BED input to gc_extrap

[nishill]

At the moment the -D switch on gc_extrap stands for both BED input and defect mode. No biggie, but it would be nice for them to have different representations.

Thanks,

[andrewdavidsmith]

Looks great -- thanks very much @nishill Can you say if this requires a change to the documentation at the same time? Or did they already assume B for BED?

[nishill]

No problem! I just checked the documentation now and it looks like the defect mode was left out of the docs for gc_extrap and the bed option is set to -D.

[timydaley]

Yup. It was a mistake on my part. Good catch nishill. Thank you very much for finding this. I guess no one had used gc_extrap with bed files and in defect mode, so the issue never came up.

[nishill]

Yeah, my use case may be fairly specific. I'm happy to help, thanks for the great software!

[timydaley]

Thank you for using it. Feel free to send any questions, ideas, or even criticisms my way. Thanks for your help.