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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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CRAM: Container and Slice states #1266

Closed jmthibault79 closed 5 years ago

jmthibault79 commented 5 years ago

Description

Add tests for Container and Slice states and associated code changes.

Related to the discussion at https://github.com/samtools/hts-specs/pull/372

Checklist

codecov-io commented 5 years ago

Codecov Report

Merging #1266 into master will increase coverage by 0.096%. The diff coverage is 94.667%.

@@               Coverage Diff               @@
##              master     #1266       +/-   ##
===============================================
+ Coverage     69.353%   69.449%   +0.096%     
- Complexity      8301      8354       +53     
===============================================
  Files            555       555               
  Lines          33116     33272      +156     
  Branches        5572      5619       +47     
===============================================
+ Hits           22967     23107      +140     
- Misses          7890      7901       +11     
- Partials        2259      2264        +5
Impacted Files Coverage Δ Complexity Δ
src/main/java/htsjdk/samtools/cram/CRAIEntry.java 71.053% <ø> (ø) 17 <0> (ø) :arrow_down:
...java/htsjdk/samtools/cram/structure/Container.java 92.105% <100%> (+7.895%) 13 <5> (+5) :arrow_up:
...samtools/cram/structure/CramCompressionRecord.java 79.167% <100%> (+2.696%) 88 <3> (+6) :arrow_up:
...a/htsjdk/samtools/cram/build/ContainerFactory.java 96.97% <100%> (+3.491%) 6 <0> (-14) :arrow_down:
...va/htsjdk/samtools/cram/build/ContainerParser.java 96.491% <100%> (+4.966%) 19 <0> (ø) :arrow_down:
...ain/java/htsjdk/samtools/cram/structure/Slice.java 60.248% <92%> (+14.713%) 38 <16> (+16) :arrow_up:
.../samtools/cram/build/CompressionHeaderFactory.java 90.11% <0%> (-0.733%) 64% <0%> (-2%)
src/main/java/htsjdk/samtools/SAMTag.java 96.667% <0%> (-0.702%) 6% <0%> (+1%)
src/main/java/htsjdk/samtools/util/Interval.java 61.818% <0%> (ø) 25% <0%> (+1%) :arrow_up:
.../main/java/htsjdk/samtools/SAMReadGroupRecord.java 97.872% <0%> (+1.321%) 72% <0%> (+29%) :arrow_up:
... and 4 more