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Fix handling of ambiguous nucleotides #148

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merged 11 commits into from
Mar 27, 2017
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ctb
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@ctb ctb commented Mar 27, 2017

This is a direct merge combining swamidass#2 + #138.

Addresses #137.

This PR updates behavior for non-ACGT nucleotides to the following:

  • k-mers containing non-ACGT are skipped when sourmash compute is run from the command line.
  • add_sequence raises an exception on k-mers containing non-ACGT, unless force is True.
  • 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?

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Codecov Report

Merging #148 into master will decrease coverage by 0.07%.
The diff coverage is 87.5%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #148      +/-   ##
==========================================
- Coverage   88.28%   88.21%   -0.08%     
==========================================
  Files          18       18              
  Lines        2348     2342       -6     
  Branches       51       52       +1     
==========================================
- Hits         2073     2066       -7     
  Misses        267      267              
- Partials        8        9       +1
Impacted Files Coverage Δ
sourmash_lib/kmer_min_hash.hh 90.28% <87.5%> (-0.88%) ⬇️

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Thanks for this!

@betatim betatim merged commit 12b50d5 into master Mar 27, 2017
@ctb ctb deleted the fix/nucleotides_update branch August 20, 2022 14:57
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4 participants