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feat: infer additional statistics from read lengths #133

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merged 6 commits into from
Aug 21, 2023

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balajtimate
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Description

  • Rewrite get_library_stats.py to infer mean, median and mode from the sample read length
  • Add additional adapter fragment sequence
  • Refactor htsinfer.py so the results print to STDOUT is now sorted in order of inference (instead of alphabetical)
  • Update logging messages and README.md
  • Downgrade Kallisto version as it was causing issues with CI

Fixes #132

Type of change

  • New feature (non-breaking change which adds functionality)

Checklist

  • I have performed a self-review of my own code
  • My code follows the existing coding style, lints and generates no new
    warnings
  • I have added type annotations to all function/method signatures, and I
    have added type annotations for any local variables that are non-trivial,
    potentially ambiguous or might otherwise benefit from explicit typing.
  • I have commented my code in hard-to-understand areas
  • I have added ["Google-style docstrings"] to all new modules, classes,
    methods/functions or updated previously existing ones
  • I have added tests that prove my fix is effective or that my feature
    works
  • New and existing unit tests pass locally with my changes and I have not
    reduced the code coverage relative to the previous state
  • I have updated any sections of the app's documentation that are affected
    by the proposed changes

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codecov bot commented Aug 21, 2023

Codecov Report

Patch coverage: 100.00% and no project coverage change.

Comparison is base (d6d892c) 99.80% compared to head (6774063) 99.80%.

Additional details and impacted files
@@           Coverage Diff           @@
##              dev     #133   +/-   ##
=======================================
  Coverage   99.80%   99.80%           
=======================================
  Files          12       12           
  Lines        1024     1039   +15     
=======================================
+ Hits         1022     1037   +15     
  Misses          2        2           
Files Changed Coverage Δ
htsinfer/htsinfer.py 100.00% <ø> (ø)
htsinfer/get_library_stats.py 100.00% <100.00%> (ø)
htsinfer/models.py 100.00% <100.00%> (ø)

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htsinfer/get_library_stats.py Outdated Show resolved Hide resolved
htsinfer/get_library_stats.py Outdated Show resolved Hide resolved
htsinfer/htsinfer.py Show resolved Hide resolved
htsinfer/models.py Outdated Show resolved Hide resolved
@balajtimate balajtimate merged commit 58d7bbf into dev Aug 21, 2023
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@balajtimate balajtimate deleted the add_length_stats branch August 21, 2023 20:33
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Expand inferred read length stats
2 participants