Olgabot/use x if codon not found

[olgabot]

This adjusts the _dna_to_aa code to fallback on the "X" if the codon was not found. Hopefully addresses #502 because std::map::operator[] inserts a new element and returns it, in this case the empty string, and then the protein kmers built on DNA seuqences with "N"s are an incorrect length because they are too short.

Can't get sourmash to install via conda on my mac laptop right now so I haven't been able to run the tests.

• Is it mergeable?
• make test Did it pass the tests?
• make coverage Is the new code covered?
• Did it change the command-line interface? Only additions are allowed
  without a major version increment. Changing file formats also requires a
  major version number increment.
• Was a spellchecker run on the source code and documentation after
  changes were made?

[codecov-io]

Codecov Report

Merging #529 into master will increase coverage by <.01%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master     #529      +/-   ##
==========================================
+ Coverage   90.76%   90.76%   +<.01%     
==========================================
  Files          33       33              
  Lines        5011     5013       +2     
  Branches       36       37       +1     
==========================================
+ Hits         4548     4550       +2     
  Misses        463      463

Impacted Files	Coverage Δ
sourmash/kmer_min_hash.hh	100% <100%> (ø)	⬆️

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[olgabot]

Any updates on this merge?

[luizirber]

quick comment: you can replace std::map<std::string,std::string>::iterator with auto and avoid having to figure out the proper type (yay C++11)

[olgabot]

Yay! Just made the change :)

[luizirber]

Hi! Why did you choose X to be the replacement? Is that the equivalent to N in amino acid code? I usually try to follow this table for conversions, but I never saw X before...
(and if it is not clear, this is me confessing my ignorance, so any pointers to other refs would be really helpful =] )

[olgabot]

Yep, X is the equivalent of N! Here's an official-looking (and Web 0.1-looking) reference: https://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/MolBioReview/iupac_aa_abbreviations.html

[luizirber]

I think this sounds reasonable, any comments @ctb ?