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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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Fixes broken XSV Indexing #1429

Closed jonn-smith closed 4 years ago

jonn-smith commented 4 years ago

Fixing XSV indexing issue.

codecov-io commented 4 years ago

Codecov Report

Merging #1429 into master will increase coverage by 0.054%. The diff coverage is 90.909%.

@@               Coverage Diff               @@
##              master     #1429       +/-   ##
===============================================
+ Coverage     68.375%   68.429%   +0.054%     
- Complexity      8486      8501       +15     
===============================================
  Files            583       583               
  Lines          34375     34446       +71     
  Branches        5732      5745       +13     
===============================================
+ Hits           23504     23571       +67     
- Misses          8650      8654        +4     
  Partials        2221      2221
Impacted Files Coverage Δ Complexity Δ
...c/main/java/htsjdk/tribble/index/IndexFactory.java 80.531% <90.909%> (+5.047%) 41 <0> (+14) :arrow_up:
...htsjdk/samtools/util/nio/DeleteOnExitPathHook.java 90.476% <0%> (+9.524%) 4% <0%> (+1%) :arrow_up:
jonn-smith commented 4 years ago

Ah. Yeah - I didn't know HTSJDK had any codecs that did this.

I'll add one here as well as my GATK test.

lbergelson commented 4 years ago

@cmnbroad @pshapiro4broad I added a test to this. Could one of you review when you get a chance?