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projectglow / glow

An open-source toolkit for large-scale genomic analysis
https://projectglow.io
Apache License 2.0
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Support whitespaces for variant datasources #475

Closed williambrandler closed 1 year ago

williambrandler commented 2 years ago

Signed-off-by: William Brandler william.brandler@databricks.com

What changes are proposed in this pull request?

VCF reader does not support special characters such as whitespaces, but json and csv datasource readers do.

Right now a user would have to replace whitespaces with underscores, which may be time consuming if the number of files to convert is large.

https://github.com/projectglow/glow/issues/474

How is this patch tested?

Will need to write unit tests to check a path with whitespaces

(Details)

codecov[bot] commented 2 years ago

Codecov Report

Merging #475 (5f4e941) into master (f9eda3e) will not change coverage. The diff coverage is 100.00%.

Impacted file tree graph

@@           Coverage Diff           @@
##           master     #475   +/-   ##
=======================================
  Coverage   93.66%   93.66%           
=======================================
  Files          95       95           
  Lines        4875     4875           
  Branches      457      467   +10     
=======================================
  Hits         4566     4566           
  Misses        309      309
Impacted Files Coverage Δ
.../main/scala/io/projectglow/vcf/VCFFileFormat.scala 97.53% <100.00%> (ø)

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