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samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.
http://samtools.github.io/htsjdk/
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Adding Locales to String.format calls #1514

Closed lbergelson closed 3 years ago

lbergelson commented 4 years ago

Setting the local to US in String.format calls that are used to generate computer readable outputs. Error messages are still written with the default local. Fix for https://github.com/samtools/htsjdk/issues/1510

lbergelson commented 4 years ago

You're right, this needs a test. I just checked manually. It's probably not perfect but it's better than nothing. I could automatically insert locals in ALL calls but it seemed like extra verbosity in most cases with no benefit.

codecov-commenter commented 4 years ago

Codecov Report

Merging #1514 into master will increase coverage by 0.014%. The diff coverage is 81.818%.

@@               Coverage Diff               @@
##              master     #1514       +/-   ##
===============================================
+ Coverage     69.343%   69.358%   +0.014%     
- Complexity      8900      8902        +2     
===============================================
  Files            601       601               
  Lines          35503     35503               
  Branches        5901      5901               
===============================================
+ Hits           24619     24624        +5     
+ Misses          8548      8544        -4     
+ Partials        2336      2335        -1
Impacted Files Coverage Δ Complexity Δ
...va/htsjdk/samtools/cram/digest/ContentDigests.java 53.465% <0.000%> (ø) 9.000 <0.000> (ø)
...java/htsjdk/samtools/cram/ref/ReferenceSource.java 46.729% <0.000%> (ø) 19.000 <0.000> (ø)
src/main/java/htsjdk/samtools/SAMUtils.java 62.802% <100.000%> (ø) 131.000 <0.000> (ø)
src/main/java/htsjdk/samtools/SamFlagField.java 92.308% <100.000%> (ø) 12.000 <0.000> (ø)
.../samtools/util/BlockCompressedFilePointerUtil.java 86.667% <100.000%> (ø) 20.000 <1.000> (ø)
...c/main/java/htsjdk/samtools/util/SequenceUtil.java 70.118% <100.000%> (ø) 130.000 <1.000> (ø)
src/main/java/htsjdk/variant/vcf/VCFEncoder.java 87.374% <100.000%> (+1.515%) 69.000 <3.000> (+1.000)
.../htsjdk/variant/variantcontext/VariantContext.java 78.373% <0.000%> (+0.370%) 238.000% <0.000%> (+1.000%)