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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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VCF 4.3 writing. #1596

Open cmnbroad opened 2 years ago

cmnbroad commented 2 years ago

Replacement for https://github.com/samtools/htsjdk/pull/1548. Depends on https://github.com/samtools/htsjdk/pull/1581, and will remain draft until https://github.com/samtools/htsjdk/pull/1581 is merged.

codecov-commenter commented 2 years ago

Codecov Report

Merging #1596 (f59a4e5) into master (347c0ac) will increase coverage by 0.086%. The diff coverage is 78.414%.

:exclamation: Current head f59a4e5 differs from pull request most recent head 0d625b7. Consider uploading reports for the commit 0d625b7 to get more accurate results

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@@               Coverage Diff               @@
##              master     #1596       +/-   ##
===============================================
+ Coverage     69.856%   69.942%   +0.086%     
- Complexity      9695      9911      +216     
===============================================
  Files            703       708        +5     
  Lines          37772     38376      +604     
  Branches        6139      6249      +110     
===============================================
+ Hits           26386     26841      +455     
- Misses          8929      9046      +117     
- Partials        2457      2489       +32
Impacted Files Coverage Δ
...in/java/htsjdk/samtools/SAMSequenceDictionary.java 75.000% <ø> (ø)
...dk/variant/variantcontext/VariantContextUtils.java 16.129% <ø> (ø)
...htsjdk/variant/vcf/VCFPassThruTextTransformer.java 50.000% <0.000%> (-50.000%) :arrow_down:
...c/main/java/htsjdk/variant/vcf/VCFRecordCodec.java 0.000% <0.000%> (ø)
src/main/java/htsjdk/variant/vcf/VCFCodec.java 21.429% <18.182%> (-55.844%) :arrow_down:
src/main/java/htsjdk/variant/vcf/VCFUtils.java 45.570% <28.571%> (-3.706%) :arrow_down:
...ta/codecs/variants/vcf/vcfv4_3/VCFDecoderV4_3.java 55.556% <33.333%> (-44.444%) :arrow_down:
src/main/java/htsjdk/variant/vcf/VCFEncoder.java 77.533% <43.750%> (-10.851%) :arrow_down:
src/main/java/htsjdk/variant/vcf/VCF3Codec.java 57.895% <50.000%> (-5.520%) :arrow_down:
...n/java/htsjdk/variant/vcf/VCFFormatHeaderLine.java 66.667% <57.895%> (-3.333%) :arrow_down:
... and 39 more

... and 30 files with indirect coverage changes