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Compress protein text using bit packing (from 8 bits per char to 5 bits) #26
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pverscha
changed the title
Text compression
Compress protein text using bit packing (from 8 bits per char to 5 bits)
Sep 19, 2024
pverscha
approved these changes
Sep 19, 2024
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Looking good!
Codecov ReportAll modified and coverable lines are covered by tests ✅
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 ☔ View full report in Codecov by Sentry. |
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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.