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Refactor GFF3 reader #65

Merged
merged 4 commits into from
May 31, 2019
Merged

Refactor GFF3 reader #65

merged 4 commits into from
May 31, 2019

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standage
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@standage standage commented May 31, 2019

This update reorganizes much of the GFF3 reader code into smaller, more modular chunks. Also, the GFF3 reader was updated to support emitting unsorted annotation components (as an optional feature). This allows efficient processing of unsorted GFF3 files, as long as they contain separator directives (###). Closes #45.

  • Full test coverage? Any additional tests that could easily be added?
  • API documentation up-to-date? Docstring examples?
  • Is the CHANGELOG up-to-date?

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codecov-io commented May 31, 2019

Codecov Report

Merging #65 into master will not change coverage.
The diff coverage is 100%.

Impacted file tree graph

@@          Coverage Diff          @@
##           master    #65   +/-   ##
=====================================
  Coverage     100%   100%           
=====================================
  Files          18     18           
  Lines        1064   1091   +27     
  Branches      250    254    +4     
=====================================
+ Hits         1064   1091   +27
Impacted Files Coverage Δ
tag/feature.py 100% <100%> (ø) ⬆️
tag/reader.py 100% <100%> (ø) ⬆️
tag/cli/gff3.py 100% <100%> (ø) ⬆️

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@standage standage merged commit 86ca8bf into master May 31, 2019
@standage standage deleted the refactor/reader branch May 31, 2019 17:54
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Split out sorting behavior to a dedicated generator
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