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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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Allow BCFCodec subclasses to provide custom version compatibility. #1352

Closed cmnbroad closed 5 years ago

cmnbroad commented 5 years ago

Fix/workaround for https://github.com/broadinstitute/gatk/issues/5839. Allows BCFCodec subclasses to override the default version compatibility policy.

codecov-io commented 5 years ago

Codecov Report

Merging #1352 into master will increase coverage by 0.014%. The diff coverage is 52.941%.

@@               Coverage Diff               @@
##              master     #1352       +/-   ##
===============================================
+ Coverage     67.848%   67.863%   +0.014%     
- Complexity      8283      8289        +6     
===============================================
  Files            563       563               
  Lines          33706     33718       +12     
  Branches        5657      5659        +2     
===============================================
+ Hits           22869     22882       +13     
+ Misses          8659      8656        -3     
- Partials        2178      2180        +2
Impacted Files Coverage Δ Complexity Δ
src/main/java/htsjdk/variant/bcf2/BCF2Codec.java 77.778% <44.444%> (+0.397%) 36 <3> (+1) :arrow_up:
src/main/java/htsjdk/variant/bcf2/BCFVersion.java 88.889% <62.5%> (-5.848%) 11 <3> (+4)
...antcontext/writer/VariantContextWriterBuilder.java 82.803% <0%> (+0.11%) 60% <0%> (ø) :arrow_down:
...samtools/util/AsyncBlockCompressedInputStream.java 76% <0%> (+4%) 13% <0%> (+1%) :arrow_up: