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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 option to hard clip reads in CigarUtils #1453

Closed fleharty closed 4 years ago

fleharty commented 4 years ago

Description

This adds the option to hard clip reads in CigarUtils.

Things to think about before submitting:

fleharty commented 4 years ago

@kachulis @lbergelson Louis, these are the changes we discussed for HTSJDK to support hard clipping. I didn't know if you would be interested in reviewing.

codecov-io commented 4 years ago

Codecov Report

Merging #1453 into master will increase coverage by 0.094%. The diff coverage is 50%.

@@              Coverage Diff               @@
##             master     #1453       +/-   ##
==============================================
+ Coverage     68.41%   68.504%   +0.094%     
- Complexity     8499      8755      +256     
==============================================
  Files           583       591        +8     
  Lines         34413     35332      +919     
  Branches       5729      5904      +175     
==============================================
+ Hits          23542     24204      +662     
- Misses         8650      8859      +209     
- Partials       2221      2269       +48
Impacted Files Coverage Δ Complexity Δ
src/main/java/htsjdk/samtools/util/CigarUtil.java 30.405% <50%> (+0.102%) 16 <15> (+2) :arrow_up:
...htsjdk/samtools/util/nio/DeleteOnExitPathHook.java 80.952% <0%> (-9.524%) 3% <0%> (-1%)
.../htsjdk/variant/utils/BinomialCoefficientUtil.java 13.131% <0%> (ø) 7% <0%> (?)
src/main/java/htsjdk/tribble/gff/Gff3Feature.java 58.333% <0%> (ø) 7% <0%> (?)
...nt/variantcontext/GenotypeNumLikelihoodsCache.java 90.625% <0%> (ø) 12% <0%> (?)
src/main/java/htsjdk/tribble/MutableFeature.java 100% <0%> (ø) 6% <0%> (?)
src/main/java/htsjdk/tribble/gff/Gff3Codec.java 76.596% <0%> (ø) 48% <0%> (?)
...c/main/java/htsjdk/tribble/gff/SequenceRegion.java 82.353% <0%> (ø) 7% <0%> (?)
.../main/java/htsjdk/tribble/gff/Gff3FeatureImpl.java 78.462% <0%> (ø) 38% <0%> (?)
src/main/java/htsjdk/tribble/gff/Gff3BaseData.java 72.917% <0%> (ø) 15% <0%> (?)
... and 4 more
davidbenjamin commented 4 years ago

@fleharty I can review this.

davidbenjamin commented 4 years ago

Good to go!

lbergelson commented 4 years ago

Replaced by #1461