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Add 1 d chunking #119
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Add 1 d chunking #119
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #119 +/- ##
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- Coverage 97.32% 96.88% -0.45%
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Files 6 7 +1
Lines 337 385 +48
Branches 56 62 +6
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+ Hits 328 373 +45
- Misses 7 8 +1
- Partials 2 4 +2
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Also switch to 32MiB chunks Closes tskit-dev#69 Closes tskit-dev#118
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I think this is ready to go in once we've validated that it actually does fix compression on very large files. I don't have an example lying around handy (raw sc2ts output triggers this, which is what's motivated me to do it!) I checked in terms of compression performance on the final sc2ts output, and the files are very slightly larger. It's not worth worrying about. |
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I can confirm that this can store columns that are this long, but there's now nasty performance gotchas with the decoding stage which depends on zarr's "iter" implementation over arrays (which is awful). I'm looking to simplify some logic in here while I'm at it, as it seems unnecessarily convoluted. |
WIP for #118