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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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Add support for re-serializing (sharding and reassembling) CRAM containers. #1609

Open cmnbroad opened 2 years ago

cmnbroad commented 2 years ago

Fixes https://github.com/samtools/htsjdk/issues/1606.

codecov-commenter commented 2 years ago

Codecov Report

Merging #1609 (fd7cb83) into master (f461401) will increase coverage by 0.028%. The diff coverage is 94.737%.

@@               Coverage Diff               @@
##              master     #1609       +/-   ##
===============================================
+ Coverage     69.838%   69.866%   +0.028%     
- Complexity      9666      9677       +11     
===============================================
  Files            703       704        +1     
  Lines          37690     37728       +38     
  Branches        6121      6124        +3     
===============================================
+ Hits           26322     26359       +37     
- Misses          8914      8916        +2     
+ Partials        2454      2453        -1
Impacted Files Coverage Δ
...a/htsjdk/samtools/CRAMContainerStreamRewriter.java 92.000% <92.000%> (ø)
...java/htsjdk/samtools/cram/structure/Container.java 84.783% <100.000%> (+0.692%) :arrow_up:
...tsjdk/samtools/cram/structure/ContainerHeader.java 86.364% <100.000%> (+0.426%) :arrow_up:
...ain/java/htsjdk/samtools/cram/structure/Slice.java 82.873% <100.000%> (+0.422%) :arrow_up:
src/main/java/htsjdk/io/AsyncWriterPool.java 72.222% <0.000%> (-1.389%) :arrow_down:
src/main/java/htsjdk/tribble/gff/Gff3BaseData.java 80.556% <0.000%> (+1.389%) :arrow_up: