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xavierdidelot / BactDating

Bayesian inference of ancestral dates on bacterial phylogenetic trees
https://xavierdidelot.github.io/BactDating
MIT License
81 stars 15 forks source link

Fix for hashes in sample names, and readGubbins file names #4

Closed johnlees closed 6 years ago

johnlees commented 6 years ago

This is a small fix for when sample names contain hashes, which are not dealt with correctly by the read.table default.

I have also reverted the change in 88af87e819385e5b9db69267893523a2c2b19092 which made the file names incorrect for the gubbins output I was using. I think this was from v1.4.9, but this may be version dependent.

codecov-io commented 6 years ago

Codecov Report

Merging #4 into master will not change coverage. The diff coverage is 0%.

Impacted file tree graph

@@           Coverage Diff           @@
##           master       #4   +/-   ##
=======================================
  Coverage   75.35%   75.35%           
=======================================
  Files           9        9           
  Lines         710      710           
=======================================
  Hits          535      535           
  Misses        175      175
Impacted Files Coverage Δ
R/loadGubbins.R 0% <0%> (ø) :arrow_up:
R/loadCFML.R 0% <0%> (ø) :arrow_up:

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xavierdidelot commented 6 years ago

Thanks John! Concerning the gubbins filename, I will add a test of which filename to use.