samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.
http://samtools.github.io/htsjdk/
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Fixes for issues found by SpotBugs #1283

Closed jmthibault79 closed 5 years ago

jmthibault79 commented 5 years ago

Description

Resolves #1279 - removed the ExternalBlock class which was not truly necessary Resolves #1280 - removed the unused CramIterator.nextRecord field Resolves #1281 - removed the unused CramHeader.clone() method

Checklist

codecov-io commented 5 years ago

Codecov Report

Merging #1283 into master will increase coverage by 0.006%. The diff coverage is 78.571%.

@@               Coverage Diff               @@
##              master     #1283       +/-   ##
===============================================
+ Coverage     67.495%   67.501%   +0.006%     
+ Complexity      8150      8149        -1     
===============================================
  Files            558       557        -1     
  Lines          33364     33352       -12     
  Branches        5608      5607        -1     
===============================================
- Hits           22519     22513        -6     
+ Misses          8657      8651        -6     
  Partials        2188      2188
Impacted Files Coverage Δ Complexity Δ
...ava/htsjdk/samtools/cram/structure/CramHeader.java 48% <ø> (+8%) 7 <0> (ø) :arrow_down:
src/main/java/htsjdk/samtools/CRAMIterator.java 81.343% <0%> (+0.184%) 32 <0> (ø) :arrow_down:
...ain/java/htsjdk/samtools/cram/structure/Slice.java 60.248% <100%> (ø) 38 <0> (ø) :arrow_down:
...va/htsjdk/samtools/cram/structure/block/Block.java 75.362% <83.333%> (+0.362%) 23 <7> (+1) :arrow_up: