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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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Some long reads tests using PacBio data. #1564

Closed cmnbroad closed 3 years ago

cmnbroad commented 3 years ago

The tests are written using the new plugin API (during which discovered that we need to add a utility method that resolves an index file name for a file that doesn't yet exist, given the file's name, but that can go into a separate PR). I have some ONT data as well but its currently too large to put in the repo.

codecov-commenter commented 3 years ago

Codecov Report

Merging #1564 (ec8e45f) into master (6a60de7) will increase coverage by 0.024%. The diff coverage is n/a.

@@               Coverage Diff               @@
##              master     #1564       +/-   ##
===============================================
+ Coverage     69.814%   69.838%   +0.024%     
- Complexity      9627      9633        +6     
===============================================
  Files            702       702               
  Lines          37607     37607               
  Branches        6107      6107               
===============================================
+ Hits           26255     26264        +9     
+ Misses          8903      8897        -6     
+ Partials        2449      2446        -3
Impacted Files Coverage Δ
...htsjdk/samtools/util/nio/DeleteOnExitPathHook.java 80.952% <0.000%> (-9.524%) :arrow_down:
src/main/java/htsjdk/samtools/SAMRecord.java 67.594% <0.000%> (+0.121%) :arrow_up:
src/main/java/htsjdk/samtools/BAMRecord.java 83.721% <0.000%> (+0.581%) :arrow_up:
src/main/java/htsjdk/samtools/Cigar.java 81.579% <0.000%> (+0.877%) :arrow_up:
src/main/java/htsjdk/samtools/Bin.java 83.673% <0.000%> (+6.122%) :arrow_up:
.../beta/codecs/reads/bam/bamV1_0/BAMEncoderV1_0.java 74.419% <0.000%> (+6.977%) :arrow_up:
.../htsjdk/beta/plugin/reads/ReadsEncoderOptions.java 80.000% <0.000%> (+13.333%) :arrow_up: