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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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Add VCFHeader javadoc #1469

Closed bbimber closed 4 years ago

bbimber commented 4 years ago

I recently got burned (my own fault) using VCFHeader.getSampleNamesInOrder(). In retrospect I should have seen it, but 'InOrder' could reasonably be interpreted to mean 'VCF order' instead of 'sorted'. This PR adds javadoc to this method to clarify.

codecov-io commented 4 years ago

Codecov Report

Merging #1469 into master will increase coverage by 0.006%. The diff coverage is n/a.

@@               Coverage Diff               @@
##              master     #1469       +/-   ##
===============================================
+ Coverage     69.196%   69.202%   +0.006%     
- Complexity      8699      8700        +1     
===============================================
  Files            587       587               
  Lines          34580     34580               
  Branches        5779      5779               
===============================================
+ Hits           23928     23930        +2     
+ Misses          8369      8368        -1     
+ Partials        2283      2282        -1
Impacted Files Coverage Δ Complexity Δ
src/main/java/htsjdk/variant/vcf/VCFHeader.java 90.116% <ø> (ø) 76 <0> (ø) :arrow_down:
...htsjdk/samtools/util/nio/DeleteOnExitPathHook.java 90.476% <0%> (+9.524%) 4% <0%> (+1%) :arrow_up:
lbergelson commented 4 years ago

@bbimber Thank you! We should have done this long ago, I can never remember what order it means without looking at the code.