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Make Validation error emit the validation type that was violated #1395

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merged 2 commits into from
Jun 27, 2019

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yfarjoun
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Validation errors are not helpful for figuring out how to ignore or fix the problem.

By emitting the Type of the validation error, this PR helps the user know which validation error needs to be ignored, or search the code to understand the problem.

Yossi Farjoun added 2 commits June 26, 2019 21:55
…ix the problem. By emitting the Type of the validation error, this PR helps the user know which validation error needs to be ignored, or search the code to understand the problem.
@yfarjoun yfarjoun requested review from lbergelson and removed request for lbergelson June 27, 2019 01:57
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codecov-io commented Jun 27, 2019

Codecov Report

Merging #1395 into master will increase coverage by 1.583%.
The diff coverage is 100%.

@@              Coverage Diff               @@
##             master     #1395       +/-   ##
==============================================
+ Coverage     68.03%   69.613%   +1.583%     
- Complexity     8368      9686     +1318     
==============================================
  Files           573       573               
  Lines         33885     38135     +4250     
  Branches       5662      6935     +1273     
==============================================
+ Hits          23052     26547     +3495     
- Misses         8643      9206      +563     
- Partials       2190      2382      +192
Impacted Files Coverage Δ Complexity Δ
.../main/java/htsjdk/samtools/SAMValidationError.java 96.154% <100%> (+0.037%) 9 <0> (ø) ⬇️
src/main/java/htsjdk/variant/vcf/VCFConstants.java 70% <0%> (-17.5%) 1% <0%> (ø)
...main/java/htsjdk/variant/vcf/VCFHeaderVersion.java 68% <0%> (-3.875%) 21% <0%> (+8%)
src/main/java/htsjdk/samtools/BAMSBIIndexer.java 73.333% <0%> (-1.667%) 1% <0%> (ø)
src/main/java/htsjdk/variant/vcf/VCFHeader.java 89.362% <0%> (-0.697%) 124% <0%> (+48%)
src/main/java/htsjdk/samtools/util/Interval.java 68.293% <0%> (-0.041%) 41% <0%> (+12%)
src/main/java/htsjdk/tribble/Tribble.java 100% <0%> (ø) 16% <0%> (+8%) ⬆️
...s/cram/encoding/external/ExternalByteEncoding.java 100% <0%> (ø) 10% <0%> (+5%) ⬆️
...ram/encoding/external/ExternalIntegerEncoding.java 100% <0%> (ø) 10% <0%> (+5%) ⬆️
src/main/java/htsjdk/tribble/util/TabixUtils.java 0% <0%> (ø) 0% <0%> (ø) ⬇️
... and 59 more

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@lbergelson lbergelson left a comment

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Good idea!

@lbergelson lbergelson merged commit 83da7e7 into master Jun 27, 2019
@lbergelson lbergelson deleted the yf_make_validation_error_actionable branch June 27, 2019 16:50
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3 participants