samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.
http://samtools.github.io/htsjdk/
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CRAM tiny refactor: remove CramCompressionRecord.tagIds #1345

Closed jmthibault79 closed 5 years ago

jmthibault79 commented 5 years ago

Checklist

jmthibault79 commented 5 years ago

It was only used inside one method. So now it's declared there.

codecov-io commented 5 years ago

Codecov Report

Merging #1345 into master will increase coverage by 0.302%. The diff coverage is 100%.

@@              Coverage Diff               @@
##              master    #1345       +/-   ##
==============================================
+ Coverage     67.848%   68.15%   +0.302%     
- Complexity      8283     8449      +166     
==============================================
  Files            563      563               
  Lines          33706    34314      +608     
  Branches        5657     5821      +164     
==============================================
+ Hits           22869    23385      +516     
- Misses          8659     8732       +73     
- Partials        2178     2197       +19
Impacted Files Coverage Δ Complexity Δ
...samtools/cram/structure/CramCompressionRecord.java 92.969% <ø> (ø) 113 <0> (ø) :arrow_down:
.../samtools/cram/build/CompressionHeaderFactory.java 90.11% <100%> (ø) 64 <0> (ø) :arrow_down:
...n/java/htsjdk/samtools/cram/structure/SliceIO.java 84.524% <0%> (+1.19%) 15% <0%> (+1%) :arrow_up:
...c/main/java/htsjdk/samtools/util/IntervalList.java 76.321% <0%> (+2.424%) 131% <0%> (+62%) :arrow_up:
...java/htsjdk/samtools/cram/structure/Container.java 91.781% <0%> (+3.737%) 31% <0%> (+4%) :arrow_up:
...samtools/util/AsyncBlockCompressedInputStream.java 76% <0%> (+4%) 13% <0%> (+1%) :arrow_up:
...ain/java/htsjdk/samtools/cram/structure/Slice.java 72.174% <0%> (+4.581%) 67% <0%> (+24%) :arrow_up:
...va/htsjdk/samtools/cram/structure/ContainerIO.java 68.056% <0%> (+4.722%) 10% <0%> (ø) :arrow_down:
...main/java/htsjdk/variant/vcf/AbstractVCFCodec.java 79.2% <0%> (+5.354%) 145% <0%> (+59%) :arrow_up:
src/main/java/htsjdk/samtools/util/Interval.java 66.667% <0%> (+5.376%) 43% <0%> (+15%) :arrow_up: