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Compress protein text using bit packing (from 8 bits per char to 5 bits) #26

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merged 13 commits into from
Sep 19, 2024

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SimonVandeVyver
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@SimonVandeVyver SimonVandeVyver commented Sep 11, 2024

Implements bit packing to only use 5 bits per amino acid in the protein text. Since there are only 20 different amino acids, 5 bits (instead of the default 8 bits per character) are sufficient to represent each amino acid. This effectively reduces the size of the text with 37.5%. We use a bit array to represent the text.

@SimonVandeVyver SimonVandeVyver self-assigned this Sep 11, 2024
@SimonVandeVyver SimonVandeVyver marked this pull request as ready for review September 13, 2024 11:42
@pverscha pverscha changed the title Text compression Compress protein text using bit packing (from 8 bits per char to 5 bits) Sep 19, 2024
@pverscha pverscha self-requested a review September 19, 2024 07:58
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Looking good!

@pverscha pverscha merged commit 4d63609 into develop Sep 19, 2024
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codecov bot commented Sep 19, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 95.18%. Comparing base (f15e3f8) to head (79bee50).
Report is 30 commits behind head on develop.

Additional details and impacted files
@@             Coverage Diff             @@
##           develop      #26      +/-   ##
===========================================
+ Coverage    94.92%   95.18%   +0.26%     
===========================================
  Files           18       18              
  Lines         1477     1350     -127     
===========================================
- Hits          1402     1285     -117     
+ Misses          75       65      -10     

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2 participants