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Fix large PLINK file ingest #135

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merged 1 commit into from
Jan 21, 2020

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karenfeng
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@karenfeng karenfeng commented Jan 17, 2020

What changes are proposed in this pull request?

Calculates the byte location for a variant in a (PLINK) BED file as a Long to avoid integer overflow.
Addresses #133.

How is this patch tested?

  • Unit tests
  • Integration tests
  • Manual tests

Successfully ran through the workflow described in the aforementioned issue.

Signed-off-by: Karen Feng <karen.feng@databricks.com>
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codecov bot commented Jan 17, 2020

Codecov Report

Merging #135 into master will increase coverage by 0.02%.
The diff coverage is 100%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #135      +/-   ##
==========================================
+ Coverage   94.77%   94.79%   +0.02%     
==========================================
  Files          82       82              
  Lines        3999     3999              
  Branches      382      380       -2     
==========================================
+ Hits         3790     3791       +1     
+ Misses        209      208       -1
Impacted Files Coverage Δ
...n/scala/io/projectglow/plink/PlinkFileFormat.scala 100% <100%> (ø) ⬆️
...scala/io/projectglow/transformers/pipe/Piper.scala 95.38% <0%> (+1.53%) ⬆️

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@karenfeng karenfeng changed the title [WIP] Fix large PLINK file ingest Fix large PLINK file ingest Jan 18, 2020
@karenfeng karenfeng merged commit d69a9d4 into projectglow:master Jan 21, 2020
@karenfeng karenfeng deleted the plink-seek-negative branch January 21, 2020 18:52
bboutkov pushed a commit to bboutkov/glow that referenced this pull request Jan 22, 2020
Signed-off-by: Karen Feng <karen.feng@databricks.com>
henrydavidge pushed a commit to henrydavidge/glow that referenced this pull request Jun 22, 2020
Signed-off-by: Karen Feng <karen.feng@databricks.com>
Signed-off-by: Henry Davidge <hhd@databricks.com>
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2 participants