samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.
http://samtools.github.io/htsjdk/
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Test ContainerIO.calculateSliceOffsetsAndSizes() and fix the slice size calculation #1326

Closed jmthibault79 closed 5 years ago

jmthibault79 commented 5 years ago

Description

Problem: calculateSliceOffsetsAndSizes() was calculating Slice.size incorrectly.

Impact: Slices created via ContainerIO.readContainer() would produce incorrect sliceByteSize values for their CRAI entries.

Checklist

codecov-io commented 5 years ago

Codecov Report

Merging #1326 into master will increase coverage by 0.018%. The diff coverage is 91.304%.

@@               Coverage Diff               @@
##              master     #1326       +/-   ##
===============================================
+ Coverage     67.804%   67.822%   +0.018%     
- Complexity      8252      8253        +1     
===============================================
  Files            562       562               
  Lines          33641     33644        +3     
  Branches        5639      5640        +1     
===============================================
+ Hits           22810     22818        +8     
+ Misses          8658      8654        -4     
+ Partials        2173      2172        -1
Impacted Files Coverage Δ Complexity Δ
...va/htsjdk/samtools/cram/structure/ContainerIO.java 62.5% <100%> (+0.772%) 12 <0> (-1) :arrow_down:
...java/htsjdk/samtools/cram/structure/Container.java 90.476% <90%> (-0.149%) 22 <2> (+2)