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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 hashCode() to classes with equals() and clean up equals() #1222

Closed jmthibault79 closed 5 years ago

jmthibault79 commented 5 years ago

Description

equals() without hashCode() is bad news. Also, some equals() have problems too.

Checklist

jmthibault79 commented 5 years ago

~Also, fix 3 classes' equals()~ Scope expanded to cover more equals()

codecov-io commented 5 years ago

Codecov Report

Merging #1222 into master will decrease coverage by 0.04%. The diff coverage is 6.78%.

@@              Coverage Diff               @@
##              master     #1222      +/-   ##
==============================================
- Coverage     69.016%   68.975%   -0.04%     
- Complexity      8066      8072       +6     
==============================================
  Files            539       539              
  Lines          32552     32587      +35     
  Branches        5488      5510      +22     
==============================================
+ Hits           22466     22477      +11     
- Misses          7890      7903      +13     
- Partials        2196      2207      +11
Impacted Files Coverage Δ Complexity Δ
src/main/java/htsjdk/tribble/index/Block.java 56.25% <0%> (-3.75%) 6 <1> (ø)
...k/samtools/cram/encoding/readfeatures/Padding.java 36.842% <0%> (-2.047%) 4 <0> (ø)
...k/samtools/cram/encoding/readfeatures/RefSkip.java 36.842% <0%> (-2.047%) 4 <0> (ø)
.../samtools/cram/encoding/readfeatures/Deletion.java 36.842% <0%> (-2.047%) 4 <0> (ø)
.../samtools/cram/encoding/readfeatures/ReadBase.java 36% <0%> (-1.5%) 5 <0> (ø)
.../java/htsjdk/tribble/index/linear/LinearIndex.java 77.907% <0%> (-0.456%) 18 <0> (ø)
.../samtools/cram/encoding/readfeatures/HardClip.java 36.842% <0%> (-2.047%) 4 <0> (ø)
...samtools/cram/encoding/readfeatures/Insertion.java 31.818% <0%> (-7.071%) 4 <0> (ø)
...amtools/cram/encoding/readfeatures/InsertBase.java 65% <0%> (-3.421%) 7 <0> (ø)
...huffman/codec/CanonicalHuffmanIntegerEncoding.java 76.923% <0%> (-8.791%) 10 <0> (ø)
... and 12 more
jmthibault79 commented 5 years ago

Restored buf @lbergelson