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Spotbugs remaining fixes #1331

Merged
merged 14 commits into from
Mar 18, 2019
Merged

Spotbugs remaining fixes #1331

merged 14 commits into from
Mar 18, 2019

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lbergelson
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Description

Rebase of #1303

Checklist

  • Code compiles correctly
  • New tests covering changes and new functionality
  • All tests passing
  • Extended the README / documentation, if necessary
  • Is not backward compatible (breaks binary or source compatibility)

tomwhite and others added 14 commits March 18, 2019 16:11
@tomwhite @lbergelson
SpotBugs
0390acc
@tomwhite @lbergelson
Ignore clone/Cloneable warning
fc3dec4
@tomwhite @lbergelson
MergingSamRecordIterator and SortingCollection are not actually Seria…
f6309fc 
…lizable.
@tomwhite @lbergelson
Remove unnecessary check (it's known that i3 > -1 at this point)
452bdf5
@tomwhite @lbergelson
Deprecate IOUtils#VCF_EXTENSIONS since it is a public mutable array.
212414e
@tomwhite @lbergelson
Ignore gc warning
a8656bd
@tomwhite @lbergelson
Ignore Thread.start() warning in constructor of AbstractAsyncWriter
3ab170b
@tomwhite @lbergelson
Ignore redundant null check in htsjdk.variant.vcf.AbstractVCFCodec
c672089
@tomwhite @lbergelson
Clarify that inherited (not outer) method hasNext() is being called b…
6482343 
…y TupleIterator
@tomwhite @lbergelson
Ignore warning in HTTPHelper about writing to a static field from an …
a5abccd 
…instance.
@tomwhite @lbergelson
Ignore test for floating point equality in Histogram and LinearIndex
09cd583
@tomwhite @lbergelson
Fix NPE
2e7f566
@tomwhite @lbergelson
Preserve existing behaviour of TextualBAMIndexWriter
a2ef207
@lbergelson
run spotBugs on travis
07510fc
@codecov-io
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codecov-io commented Mar 18, 2019 •
edited
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Codecov Report

Merging #1331 into master will decrease coverage by 0.007%.
The diff coverage is 63.636%.

@@               Coverage Diff               @@
##              master     #1331       +/-   ##
===============================================
- Coverage     67.802%   67.795%   -0.007%     
+ Complexity      8252      8251        -1     
===============================================
  Files            562       562               
  Lines          33639     33641        +2     
  Branches        5641      5639        -2     
===============================================
- Hits           22808     22807        -1     
- Misses          8657      8660        +3     
  Partials        2174      2174
Impacted Files Coverage Δ Complexity Δ
...java/htsjdk/samtools/MergingSamRecordIterator.java 59.494% <100%> (ø) 19 <0> (ø) ⬇️
...ava/htsjdk/samtools/cram/compression/rans/E14.java 90.566% <100%> (+1.887%) 3 <0> (ø) ⬇️
src/main/java/htsjdk/samtools/util/IOUtil.java 58.213% <100%> (+0.101%) 118 <0> (ø) ⬇️
...n/java/htsjdk/samtools/util/SortingCollection.java 64.444% <100%> (ø) 16 <0> (ø) ⬇️
...tsjdk/tribble/readers/AsciiLineReaderIterator.java 84% <100%> (ø) 6 <0> (ø) ⬇️
...in/java/htsjdk/samtools/TextualBAMIndexWriter.java 66.667% <20%> (-0.866%) 12 <0> (ø)
...samtools/util/AsyncBlockCompressedInputStream.java 72% <0%> (-4%) 12% <0%> (-1%)

@lbergelson lbergelson merged commit 7925166 into master Mar 18, 2019
@lbergelson lbergelson deleted the spotbugs-remaining-fixes branch March 18, 2019 21:50
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@tomwhite Thank you!

@lbergelson lbergelson mentioned this pull request Mar 18, 2019
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3 participants
@lbergelson @codecov-io @tomwhite