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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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- Expand SamLocusAndReferenceIterator tests to cover BAMs and CRAMs. #1521

Open yfarjoun opened 3 years ago

yfarjoun commented 3 years ago

(Sorry about the premature push into master earlier)

There seems to be a lack of testing of SamLocusAndReferenceIterator on cram and bam files, which lead one of our contributors to submit #1483 which seems to be solving a problem that doesn't exist. I hope that this PR will provide an example of how to properly create a SamLocusAndReferenceIterator in a way that is agnostic of the type of file (sam/bam/cram) at hand.

codecov-io commented 3 years ago

Codecov Report

Merging #1521 (90f979b) into master (2c4c9b2) will decrease coverage by 0.001%. The diff coverage is 62.500%.

@@               Coverage Diff               @@
##              master     #1521       +/-   ##
===============================================
- Coverage     69.404%   69.404%   -0.001%     
- Complexity      8920      8925        +5     
===============================================
  Files            601       602        +1     
  Lines          35515     35534       +19     
  Branches        5904      5909        +5     
===============================================
+ Hits           24649     24662       +13     
- Misses          8532      8534        +2     
- Partials        2334      2338        +4
Impacted Files Coverage Δ Complexity Δ
src/main/java/htsjdk/samtools/BamFileIoUtils.java 1.235% <0.000%> (ø) 3.000 <0.000> (ø)
src/main/java/htsjdk/samtools/CRAMFileReader.java 75.000% <0.000%> (ø) 45.000 <0.000> (ø)
...mtools/reference/SamLocusAndReferenceIterator.java 100.000% <ø> (ø) 5.000 <0.000> (ø)
...main/java/htsjdk/samtools/util/FileExtensions.java 80.000% <ø> (ø) 1.000 <0.000> (ø)
src/main/java/htsjdk/samtools/util/TestUtil.java 55.263% <60.000%> (+5.263%) 4.000 <2.000> (+2.000)
src/main/java/htsjdk/samtools/BAMFileReader.java 69.501% <100.000%> (ø) 50.000 <0.000> (ø)
src/main/java/htsjdk/samtools/BAMFileWriter.java 66.667% <100.000%> (ø) 17.000 <0.000> (ø)
...ain/java/htsjdk/samtools/SAMFileWriterFactory.java 67.097% <100.000%> (ø) 50.000 <0.000> (ø)
src/main/java/htsjdk/samtools/SamFiles.java 92.683% <100.000%> (ø) 15.000 <0.000> (ø)
src/main/java/htsjdk/samtools/SamIndexes.java 73.077% <100.000%> (ø) 13.000 <0.000> (ø)
... and 1 more
yfarjoun commented 3 years ago

back to you @lbergelson