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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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Build and test on java 11 #1291

Closed lbergelson closed 5 years ago

lbergelson commented 5 years ago

Description

This is an extension of #1269 which resolves some problems with the build in gradle 5+

Checklist

lbergelson commented 5 years ago

@cmnbroad Could you take a look at this when you get a chance? It has a bunch of gradle changes because the maven publishing plugin broke when we moved to gradle 5 and rather than figure out what was going wrong I updated it to use the maven-publish plugin instead which is the new recommended one.

codecov-io commented 5 years ago

Codecov Report

Merging #1291 into master will increase coverage by 0.016%. The diff coverage is n/a.

@@               Coverage Diff               @@
##              master     #1291       +/-   ##
===============================================
+ Coverage     67.495%   67.511%   +0.016%     
  Complexity      8150      8150               
===============================================
  Files            558       558               
  Lines          33364     33396       +32     
  Branches        5608      5632       +24     
===============================================
+ Hits           22519     22546       +27     
- Misses          8657      8666        +9     
+ Partials        2188      2184        -4
Impacted Files Coverage Δ Complexity Δ
...ain/java/htsjdk/samtools/util/MergingIterator.java 85.714% <ø> (ø) 11 <0> (ø) :arrow_down:
...c/main/java/htsjdk/samtools/util/SnappyLoader.java 78.571% <0%> (-2.198%) 9% <0%> (ø)
src/main/java/htsjdk/samtools/SamReader.java 81.818% <0%> (-0.94%) 0% <0%> (ø)
src/main/java/htsjdk/samtools/util/CigarUtil.java 30.303% <0%> (-0.466%) 14% <0%> (ø)
...java/htsjdk/samtools/cram/ref/ReferenceSource.java 46.364% <0%> (-0.425%) 19% <0%> (ø)
...htsjdk/tribble/readers/LongLineBufferedReader.java 29.944% <0%> (-0.342%) 15% <0%> (ø)
src/main/java/htsjdk/samtools/BamFileIoUtils.java 2.439% <0%> (-0.03%) 3% <0%> (ø)
...ain/java/htsjdk/samtools/SAMFileWriterFactory.java 67.296% <0%> (-0.012%) 50% <0%> (ø)
...riant/variantcontext/VariantContextComparator.java 0% <0%> (ø) 0% <0%> (ø) :arrow_down:
...t/variantcontext/filter/GenotypeQualityFilter.java 100% <0%> (ø) 7% <0%> (ø) :arrow_down:
... and 14 more