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Memory optimisation: don't store whole build array #19

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merged 5 commits into from
Feb 18, 2023

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johnlees
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Simple change: combine build and merge steps so whole array of ska_dict are not stored in memory. On 28 Listeria (3228084, 38Mb skf file)
before:
1 thread 11s, 2.3Gb
8 threads 5s, 3Gb

after:
1 thread 8s, 500Mb
2 threads (max) 6s, 890 Mb

Closes #17 (but more ideas there to further reduce memory if ever needed)

@johnlees
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TODO: fix the clippy lints

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codecov bot commented Feb 18, 2023

Codecov Report

Base: 82.02% // Head: 82.11% // Increases project coverage by +0.09% 🎉

Coverage data is based on head (203d780) compared to base (d777060).
Patch coverage: 87.50% of modified lines in pull request are covered.

Additional details and impacted files
@@            Coverage Diff             @@
##           master      #19      +/-   ##
==========================================
+ Coverage   82.02%   82.11%   +0.09%     
==========================================
  Files          15       15              
  Lines        1513     1510       -3     
  Branches      264      265       +1     
==========================================
- Hits         1241     1240       -1     
+ Misses        108      104       -4     
- Partials      164      166       +2     
Impacted Files Coverage Δ
src/ska_dict/split_kmer.rs 86.13% <ø> (-0.20%) ⬇️
src/ska_ref.rs 85.62% <ø> (-0.18%) ⬇️
src/cli.rs 67.96% <57.14%> (-0.69%) ⬇️
src/lib.rs 72.88% <89.28%> (-0.24%) ⬇️
src/merge_ska_dict.rs 80.53% <90.00%> (+2.97%) ⬆️
src/io_utils.rs 84.90% <100.00%> (+0.29%) ⬆️
src/ska_dict.rs 86.15% <100.00%> (ø)
src/generic_modes.rs 71.42% <0.00%> (-0.88%) ⬇️
... and 4 more

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@johnlees johnlees merged commit ba5b0d2 into master Feb 18, 2023
@johnlees johnlees deleted the unbuffered-merge branch February 18, 2023 17:55
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Alternatives for .skf format
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