[MRG] "consume_masked" mode for consume_seqfile_with_mask

[standage]

In branch feature/mask-comp I implemented a new complement consume_masked option for the consume_seqfile_with_mask method. By default, the function will not count any k-mers present in the mask, but with complement=True consume_masked=True the function will count only the k-mers present in the mask/filter.

In that branch I also putzed around with some Python code (utils and scripts) to get that functionality working in abundance-dist-single.py.

This PR splits the C++/Cython changes from the Python changes, the latter of which aren't ready for review yet. The C++/Cython functionality is blocking my progress on a feature in kevlar, whereas I don't have a pressing need to bake this in to khmer scripts at the moment.

• Is any new functionality in tested? (This can be checked with
  make clean diff-cover or the CodeCov report that is automatically
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[standage]

Ready for review and merge! @betatim @camillescott @ctb @luizirber

[ctb]

Hi @standage the code looks good but I am not sure why you chose complement here. I can't find a definition of the word that makes sense with the usage here - help?

[standage]

I explained this briefly in the first paragraph of the PR, but I am open to using different terminology for the variable names if it communicates intent more clearly.

The old behavior of consume_seqfile_with_mask is IMO pretty self explanatory: consume all k-mers except those in the mask. The new behavior is an option that complements this behavior, consuming all k-mers that are in the mask.

Let me know what you think regarding terminology.

[ctb]

I finally remembered to search for "set complement" and that is the right definition :). Glad I found it! What about consume_masked=True|False (False by default)?

[standage]

What about consume_masked=True|False (False by default)?

Roger that. I like it.

[ctb]

Thanks!

[standage]

Thank you