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tzcoolman / FACS-OLD

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Usability for non-scripting users #15

Closed henrikstranneheim closed 11 years ago

henrikstranneheim commented 12 years ago
  1. I want to be able to build many bloom filters by supplying a list of references or a dir. Since not everyone can do shell scripting, we should facilitate for users unaccustomed with scripting.
  2. I want to be able to check a list/dir of references for contamination and get a statistics for the complete data set as well as for each individual reference.
  3. I want to be able to remove contaminated reads by supplying a list/dir of references to be checked and get a statistics for the complete data set as well as for each individual reference.

As it is now, you can only do 1 file at a time and have to use many script calls and then compile the data yourself, which is not user friendly. I think you should be able to choose if you want to do a list (or directory ) or 1 file.

It also has implication on the remove script since you might want to check all references and classify a contamination to the reference that has the highest score. That is most easily done if you test all references with 1 call.

brainstorm commented 12 years ago

I think that both options should be available to the user: -r & -o for single files and -l for lists. What I think it's wrong is to only provide "-l" since it's not script-friendly in that case.

brainstorm commented 11 years ago

I would mark this issue as a duplicate of issue #14, Enze, can you please close it?

Thanks!