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SciLifeLab / facs

Fast and Accurate Classification of Sequences using Bloom filters
http://facs.scilifelab.se/
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facs remove -h #15

Closed henrikstranneheim closed 11 years ago

henrikstranneheim commented 11 years ago
  1. Header says "---contamination remove---". Should say "---facs remove---".
  2. Tolerant rate is perhaps not ideal. Maybe threshold value is a better name.
  3. (The program will automatically select a value if you don't provide any.) I would prefer: The program will automatically estimate a proper threshold value from the reference size and K-mer length.
  4. -l a list containing all bloom files. --> - l a list containing all Bloom filter names in....and then what the list format should be.
  5. -r reference bloom filter file or dir --> -r Bloom filter file or directory
  6. !!! either -r or -l can only be allowed each time !!!. See build issue!
brainstorm commented 11 years ago

Solved in pullrequest #17, please @tzcoolman make sure I did not miss any of @henrikstranneheim points here.

Actually, now that I look at it, I think the mutually exclusive flags should be implemented still (-r -l).

tzcoolman commented 11 years ago

Yes... @henrikstranneheim @brainstorm I verified that.. it is good

henrikstranneheim commented 11 years ago

Why is this option added to remove: -r input list containing all reference files, one per line

I see you still went with the tolerant rate instead of threshold value, but this tolerant rate seems far of: -t tolerance rate, default is 0.0005

I think we should spell bloom with a capital B e.g. Bloom.