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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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SubstitutionMatrix class cleanup - part 1. #1366

Closed cmnbroad closed 5 years ago

cmnbroad commented 5 years ago

This is mostly comments documenting what this code is doing, and some name changes, but there are no functional changes. A separate follow-on PR will pick up where this one ends.

codecov-io commented 5 years ago

Codecov Report

Merging #1366 into master will increase coverage by 0.005%. The diff coverage is 96.296%.

@@               Coverage Diff               @@
##              master     #1366       +/-   ##
===============================================
+ Coverage     67.863%   67.868%   +0.005%     
+ Complexity      8289      8286        -3     
===============================================
  Files            563       563               
  Lines          33718     33714        -4     
  Branches        5659      5651        -8     
===============================================
- Hits           22882     22881        -1     
+ Misses          8656      8652        -4     
- Partials        2180      2181        +1
Impacted Files Coverage Δ Complexity Δ
...dk/samtools/cram/structure/SubstitutionMatrix.java 91.753% <96.296%> (+0.448%) 15 <15> (ø) :arrow_down:
...c/main/java/htsjdk/samtools/util/IntervalList.java 72.18% <0%> (-1.717%) 64% <0%> (-5%)
...in/java/htsjdk/samtools/SAMSequenceDictionary.java 74.648% <0%> (-0.177%) 45% <0%> (-1%)
...c/main/java/htsjdk/samtools/SAMSequenceRecord.java 80.556% <0%> (ø) 36% <0%> (ø) :arrow_down:
src/main/java/htsjdk/samtools/util/Interval.java 63.333% <0%> (+2.043%) 28% <0%> (ø) :arrow_down:
src/main/java/htsjdk/utils/ValidationUtils.java 56% <0%> (+16%) 9% <0%> (+3%) :arrow_up: