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New getrefr module #30

Merged
merged 9 commits into from
May 20, 2019
Merged

New getrefr module #30

merged 9 commits into from
May 20, 2019

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standage
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This update introduces a new module for downloading the human reference genome into a dedicated "package data" directory. This replaces the current sub-optimal behavior of requiring the user to have a specifically-named reference genome file in the current working directory.

By default mhpl8r getrefr will download the genome directly from UCSC, but it also supports "installing" a previously downloaded copy from a local file path.

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codecov-io commented May 20, 2019

Codecov Report

Merging #30 into master will decrease coverage by 5.18%.
The diff coverage is 43.54%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master      #30      +/-   ##
==========================================
- Coverage   98.16%   92.97%   -5.19%     
==========================================
  Files          17       19       +2     
  Lines         600      655      +55     
  Branches      114      118       +4     
==========================================
+ Hits          589      609      +20     
- Misses          4       39      +35     
  Partials        7        7
Impacted Files Coverage Δ
microhapulator/cli/sim.py 100% <ø> (ø) ⬆️
microhapulator/cli/mixture.py 100% <ø> (ø) ⬆️
microhapulator/cli/refr.py 100% <ø> (ø) ⬆️
microhapulator/refr.py 100% <100%> (ø) ⬆️
microhapulator/mixture.py 100% <100%> (ø) ⬆️
microhapulator/sim.py 97.5% <100%> (ø) ⬆️
microhapulator/cli/__init__.py 93.75% <100%> (+0.2%) ⬆️
microhapulator/__init__.py 100% <100%> (ø) ⬆️
microhapulator/cli/getrefr.py 100% <100%> (ø)
microhapulator/getrefr.py 23.91% <23.91%> (ø)
... and 2 more

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@standage standage merged commit e5b626b into master May 20, 2019
@standage standage deleted the downref branch May 24, 2019 13:53
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2 participants