GMOD / bam-js

Parse BAM and BAM index files in javascript for node and the browser
MIT License
20 stars 9 forks source link

Restore chunk cache for speed improvements #89

Closed cmdcolin closed 2 years ago

cmdcolin commented 2 years ago

Restores the reloading of chunk caching. It was removed without well documented reason, possibly assuming the the unzipping was a minority of the time or that not storing the unzipped content would reduce memory usage (which may be true) but it is faster to keep the cache as jbrowse repeatedly requests the same blocks for the neighboring block based tracks

codecov[bot] commented 2 years ago

Codecov Report

Merging #89 (3f6a580) into master (2e76f0e) will decrease coverage by 0.11%. The diff coverage is 98.59%.

:exclamation: Current head 3f6a580 differs from pull request most recent head 6008300. Consider uploading reports for the commit 6008300 to get more accurate results

@@            Coverage Diff             @@
##           master      #89      +/-   ##
==========================================
- Coverage   82.24%   82.13%   -0.12%     
==========================================
  Files          13       13              
  Lines        1104     1086      -18     
  Branches      230      225       -5     
==========================================
- Hits          908      892      -16     
+ Misses        196      194       -2     
Impacted Files Coverage Δ
src/record.ts 76.96% <83.33%> (-0.16%) :arrow_down:
src/bamFile.ts 89.38% <100.00%> (-0.43%) :arrow_down:
src/htsget.ts 92.18% <0.00%> (+3.12%) :arrow_up:

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cmdcolin commented 2 years ago

Approx performance gains

deep coverage short reads

ultra long reads 80x coverage