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Upgrade to samtools 1.14. #1583

Merged
merged 2 commits into from
Dec 8, 2021
Merged

Upgrade to samtools 1.14. #1583

merged 2 commits into from
Dec 8, 2021

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cmnbroad
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@cmnbroad cmnbroad force-pushed the cn_upgrade_samtools branch from 6c0710c to c801eba Compare November 29, 2021 15:32
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codecov-commenter commented Nov 29, 2021

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%) ⬇️
...sjdk/samtools/util/htsget/HtsgetErrorResponse.java 73.333% <0.000%> (-6.667%) ⬇️
...tools/cram/encoding/core/GammaIntegerEncoding.java 86.667% <0.000%> (-6.667%) ⬇️
.../samtools/cram/compression/ExternalCompressor.java 69.565% <0.000%> (-4.509%) ⬇️
...mtools/cram/encoding/core/BetaIntegerEncoding.java 91.304% <0.000%> (-4.348%) ⬇️
...am/encoding/core/CanonicalHuffmanByteEncoding.java 52.941% <0.000%> (-2.941%) ⬇️
...ing/core/huffmanUtils/HuffmanParamsCalculator.java 80.000% <0.000%> (-1.818%) ⬇️
...va/htsjdk/samtools/util/htsget/HtsgetResponse.java 89.394% <0.000%> (-1.783%) ⬇️
...java/htsjdk/beta/codecs/variants/vcf/VCFCodec.java 81.818% <0.000%> (-1.515%) ⬇️
...va/htsjdk/beta/codecs/variants/vcf/VCFDecoder.java 63.750% <0.000%> (-1.310%) ⬇️
... and 41 more

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👍 Is there anything interesting about the changed cram file?

@lbergelson lbergelson merged commit c0b61a2 into master Dec 8, 2021
@lbergelson lbergelson deleted the cn_upgrade_samtools branch December 8, 2021 18:18
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3 participants