Allow hamming circle around N

[tp2750]

Allow hamming circle around N

This fixes #124 : Demultiplexer fails for Levenshtein distance > 1

The problem was that the levenshtein_circle function generates sequences containing N, but the hamming_circle function was not able to create a circle around those.

With this change, the circle around N is created as [A,C,G,T]

Types of changes

This PR implements the following changes:
(Please tick any or all of the following that are applicable)

• ✨ New feature (A non-breaking change which adds functionality).
• 🐛 Bug fix (A non-breaking change, which fixes an issue).
• 💥 Breaking change (fix or feature that would cause existing functionality to change).

📋 Additional detail

Before the change:

julia> BioSequences.hamming_circle(dna"N",1)
ERROR: MethodError: no method matching isless(::Nothing, ::Int64)
Closest candidates are:
  isless(::Missing, ::Any) at missing.jl:87
  isless(::AbstractFloat, ::Real) at operators.jl:167
  isless(::Real, ::Real) at operators.jl:355
  ...
Stacktrace:
 [1] <(::Nothing, ::Int64) at /opt/Julia/julia-1.5.2/share/julia/base/operators.jl:277
 [2] <=(::Nothing, ::Int64) at /opt/Julia/julia-1.5.2/share/julia/base/operators.jl:326
 [3] hamming_circle(::LongSequence{DNAAlphabet{4}}, ::Int64) at /home/tp/Julia/Pull/2020-10-31_demultiplex/BioSequences.jl/src/demultiplexer.jl:240
 [4] top-level scope at REPL[41]:1

With change

julia> BioSequences.hamming_circle(dna"N",1)
4-element Array{LongSequence{DNAAlphabet{4}},1}:
 A
 C
 G
 T

☑️ Checklist

• 🎨 The changes implemented is consistent with the julia style guide.
• 📘 I have updated and added relevant docstrings, in a manner consistent with the documentation styleguide.
• 📘 I have added or updated relevant user and developer manuals/documentation in docs/src/.
• 🆗 There are unit tests that cover the code changes I have made.
• 🆗 The unit tests cover my code changes AND they pass.
• 📝 I have added an entry to the [UNRELEASED] section of the manually curated CHANGELOG.md file for this repository.
• 🆗 All changes should be compatible with the latest stable version of Julia.
• [] 💭 I have commented liberally for any complex pieces of internal code.

[codecov]

Codecov Report

Merging #126 (4e1bda1) into master (6f0e437) will decrease coverage by 0.00%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #126      +/-   ##
==========================================
- Coverage   83.21%   83.20%   -0.01%     
==========================================
  Files          44       44              
  Lines        2949     2948       -1     
==========================================
- Hits         2454     2453       -1     
  Misses        495      495              

Flag	Coverage Δ
unittests	83.20% <100.00%> (-0.01%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
src/demultiplexer.jl	94.25% <100.00%> (ø)
src/biosequence/indexing.jl	87.03% <0.00%> (-0.24%)	⬇️

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[tp2750]

This is a very small change, but it will have a large impact by fixing #124 .

Is there something more I can do to help it get merged?

[kescobo]

Thanks for the detailed bu
g report and PR! We appreciate the work! I don't have a good sense of the implications of this change, so I'll wait on @benjward (or maybe @jakobnissen ??) to review. Don't hesitate to bump if this doesn't get a look in a reasonable amount of time (defined however makes sense to you :-) )

[TransGirlCodes]

Thanks @tp2750