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BioJulia / GenomeGraphs.jl

A modern genomics framework for julia
https://biojulia.dev
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Basic serial, in memory kmer counting #14

Closed TransGirlCodes closed 5 years ago

TransGirlCodes commented 5 years ago

Added an internal method BioSequenceGraphs.build_freq_list for serial, in memory kmer counting of a paired-reads datastore - as input for building a DBG. It can deal with something like ecoli. Your mileage may vary. Multi-process and disk-batch-based counting is coming v. soon.

codecov[bot] commented 5 years ago

Codecov Report

:exclamation: No coverage uploaded for pull request base (benjward/workspace@7c756ab). Click here to learn what that means. The diff coverage is 28.4%.

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@@                 Coverage Diff                  @@
##             benjward/workspace     #14   +/-   ##
====================================================
  Coverage                      ?   5.53%           
====================================================
  Files                         ?      18           
  Lines                         ?     958           
  Branches                      ?       0           
====================================================
  Hits                          ?      53           
  Misses                        ?     905           
  Partials                      ?       0
Impacted Files Coverage Δ
src/BioSequenceGraphs.jl 100% <ø> (ø)
src/mertools/counting.jl 0% <0%> (ø)
src/datastores/kmer-counts.jl 0% <0%> (ø)
src/mertools/MerFreq.jl 55.55% <55.55%> (ø)

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