samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.
http://samtools.github.io/htsjdk/
283 stars 242 forks source link

more changes to SAMTagUtil #1227

Closed lbergelson closed 5 years ago

lbergelson commented 5 years ago

Checklist

codecov-io commented 5 years ago

Codecov Report

Merging #1227 into master will decrease coverage by 0.198%. The diff coverage is 26.316%.

@@               Coverage Diff               @@
##              master     #1227       +/-   ##
===============================================
- Coverage     69.031%   68.832%   -0.198%     
+ Complexity      8077      8074        -3     
===============================================
  Files            539       539               
  Lines          32616     32617        +1     
  Branches        5510      5510               
===============================================
- Hits           22515     22451       -64     
- Misses          7894      7959       +65     
  Partials        2207      2207
Impacted Files Coverage Δ Complexity Δ
...c/main/java/htsjdk/samtools/sra/SRALazyRecord.java 71.591% <0%> (ø) 130 <0> (ø) :arrow_down:
src/main/java/htsjdk/samtools/SAMTagUtil.java 0% <0%> (-98.649%) 0 <0> (-5)
...ain/java/htsjdk/samtools/cram/structure/Slice.java 44.545% <0%> (ø) 20 <0> (ø) :arrow_down:
src/main/java/htsjdk/samtools/SAMTag.java 97.368% <100%> (+0.353%) 5 <2> (+2) :arrow_up:
...n/java/htsjdk/samtools/cram/structure/SliceIO.java 88.889% <100%> (ø) 15 <0> (ø) :arrow_down:
...ain/java/htsjdk/samtools/SAMBinaryTagAndValue.java 84.884% <100%> (ø) 54 <0> (ø) :arrow_down:
...n/java/htsjdk/samtools/cram/structure/ReadTag.java 70.563% <100%> (ø) 65 <0> (ø) :arrow_down:
...dk/samtools/SAMBinaryTagAndUnsignedArrayValue.java 69.231% <100%> (ø) 5 <0> (ø) :arrow_down:
...va/htsjdk/samtools/cram/digest/ContentDigests.java 50.467% <50%> (ø) 9 <0> (ø) :arrow_down:
src/main/java/htsjdk/samtools/SAMTextWriter.java 66.292% <50%> (ø) 12 <0> (ø) :arrow_down:
... and 3 more
lbergelson commented 5 years ago

@cmnbroad Could you take a look at this? I just deprecated the SamTagUtil entirely and moved all the functionality to SAMTag so that we wouldn't have this weird split between them.

lbergelson commented 5 years ago

@pshapiro4broad @cmnbroad Thank you for the reviews!