Add -B for BED input to gc_extrap#34
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timydaley merged 1 commit intosmithlabcode:masterfrom Mar 12, 2018
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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? |
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Author
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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. |
Contributor
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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. |
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Author
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Yeah, my use case may be fairly specific. I'm happy to help, thanks for the great software! |
Contributor
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Thank you for using it. Feel free to send any questions, ideas, or even criticisms my way. Thanks for your help. |
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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,