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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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Fix IndexFactory on non-default file system. #1449

Closed cmnbroad closed 4 years ago

cmnbroad commented 4 years ago

Fixes the issue seen here, along with a new test that fails without the fix. The actual fix is a one line change, the rest of the changes are to fix error messages, and there is a second commit with some other redundant code removed.

codecov-io commented 4 years ago

Codecov Report

Merging #1449 into master will increase coverage by 0.009%. The diff coverage is 37.5%.

@@               Coverage Diff               @@
##              master     #1449       +/-   ##
===============================================
+ Coverage     68.396%   68.404%   +0.009%     
- Complexity      8497      8498        +1     
===============================================
  Files            583       583               
  Lines          34413     34413               
  Branches        5729      5729               
===============================================
+ Hits           23537     23540        +3     
+ Misses          8653      8651        -2     
+ Partials        2223      2222        -1
Impacted Files Coverage Δ Complexity Δ
...c/main/java/htsjdk/tribble/index/IndexFactory.java 74.269% <37.5%> (ø) 33 <0> (ø) :arrow_down:
src/main/java/htsjdk/samtools/BAMFileReader.java 68.466% <0%> (+0.852%) 52% <0%> (+1%) :arrow_up:
cmnbroad commented 4 years ago

Thanks for the quick review @lbergelson.