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smithlabcode / preseq

Software for predicting library complexity and genome coverage in high-throughput sequencing.
https://preseq.readthedocs.io
GNU General Public License v3.0
78 stars 16 forks source link

Add -B for BED input to gc_extrap #34

Closed nishill closed 6 years ago

nishill commented 6 years ago

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 commented 6 years ago

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 commented 6 years ago

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 commented 6 years ago

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 commented 6 years ago

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

timydaley commented 6 years ago

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