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Expose Expressions::evaluate_cell as TileDB api for use in GenomicsDB #149

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merged 6 commits into from
May 8, 2023

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nalinigans
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@nalinigans nalinigans commented May 2, 2023

Previously, tiledb_array_read api was doing the read and filtering out the cells that did not match the applied expression before returning the results in the buffers. This was not working very well when there were overflowed buffers. We now just expose the Expressions::evaluate_cell for the client to evaluate on a per cell basis directly instead of relying on tiledb_array_read to read and evaluate. This seems to be working well with the SingleCellTileDBIterator in GenomicsDB.

Also added custom muparserx operator &= for GT type of operations, e.g GT &= "00" or GT &= "0/0" or `GT &= "0|0".

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codecov bot commented May 2, 2023

Codecov Report

Merging #149 (5bf6703) into develop (e929006) will increase coverage by 0.09%.
The diff coverage is 74.35%.

@@             Coverage Diff             @@
##           develop     #149      +/-   ##
===========================================
+ Coverage    63.35%   63.44%   +0.09%     
===========================================
  Files           58       58              
  Lines        16195    16227      +32     
  Branches      2881     2887       +6     
===========================================
+ Hits         10260    10295      +35     
+ Misses        5803     5802       -1     
+ Partials       132      130       -2     
Impacted Files Coverage Δ
core/include/c_api/tiledb.h 100.00% <ø> (ø)
core/src/array/array.cc 58.70% <62.50%> (+0.68%) ⬆️
core/include/expressions/expression.h 83.54% <71.42%> (-3.13%) ⬇️
core/src/c_api/tiledb.cc 44.37% <85.71%> (+0.75%) ⬆️
core/src/expressions/expression.cc 93.48% <100.00%> (+0.07%) ⬆️

... and 4 files with indirect coverage changes

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…string of integers optionally delimited by '|' or '/'
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@mlathara mlathara left a comment

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looks good

@nalinigans nalinigans merged commit 15b8a12 into develop May 8, 2023
38 checks passed
@nalinigans nalinigans deleted the ng_expr_05012023 branch May 8, 2023 14:58
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2 participants