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MikeAxtell / ShortStack

ShortStack: Comprehensive annotation and quantification of small RNA genes
MIT License
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Inconsistencies Between Default Settings in Documentation and Code #148

Closed spriego closed 3 months ago

spriego commented 5 months ago

Dear Mike,

I've noticed some discrepancies between the default settings outlined in ShortStack's documentation and the actual code:

  1. In the documentation, --mmap is listed as defaulting to f, but in the code (line 535), it's actually set to u.
  2. Regarding --mincov, the documentation indicates a default value of 2, yet in the code (line 601), it's set to 1.
MikeAxtell commented 3 months ago

Thanks for pointing these errors out. I've updated the README to correct them.

The --mmap setting of u is the true default, and it is the superior setting according to our previous work https://doi.org/10.1534/g3.116.030452 ... so it was just the README that was wrong, not the software.