samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.
http://samtools.github.io/htsjdk/
283 stars 242 forks source link

Upgrade to samtools 1.14. #1583

Closed cmnbroad closed 2 years ago

codecov-commenter commented 2 years ago

Codecov Report

Merging #1583 (923abeb) into master (e63c34a) will decrease coverage by 0.057%. The diff coverage is n/a.

@@               Coverage Diff               @@
##              master     #1583       +/-   ##
===============================================
- Coverage     69.843%   69.786%   -0.057%     
+ Complexity      9644      9638        -6     
===============================================
  Files            702       702               
  Lines          37623     37516      -107     
  Branches        6111      6074       -37     
===============================================
- Hits           26277     26181       -96     
+ Misses          8901      8881       -20     
- Partials        2445      2454        +9     
Impacted Files Coverage Δ
...htsjdk/samtools/util/nio/DeleteOnExitPathHook.java 80.952% <0.000%> (-9.524%) :arrow_down:
...sjdk/samtools/util/htsget/HtsgetErrorResponse.java 73.333% <0.000%> (-6.667%) :arrow_down:
...tools/cram/encoding/core/GammaIntegerEncoding.java 86.667% <0.000%> (-6.667%) :arrow_down:
.../samtools/cram/compression/ExternalCompressor.java 69.565% <0.000%> (-4.509%) :arrow_down:
...mtools/cram/encoding/core/BetaIntegerEncoding.java 91.304% <0.000%> (-4.348%) :arrow_down:
...am/encoding/core/CanonicalHuffmanByteEncoding.java 52.941% <0.000%> (-2.941%) :arrow_down:
...ing/core/huffmanUtils/HuffmanParamsCalculator.java 80.000% <0.000%> (-1.818%) :arrow_down:
...va/htsjdk/samtools/util/htsget/HtsgetResponse.java 89.394% <0.000%> (-1.783%) :arrow_down:
...java/htsjdk/beta/codecs/variants/vcf/VCFCodec.java 81.818% <0.000%> (-1.515%) :arrow_down:
...va/htsjdk/beta/codecs/variants/vcf/VCFDecoder.java 63.750% <0.000%> (-1.310%) :arrow_down:
... and 41 more