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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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Path-enable IndexFactory. #1430

Closed cmnbroad closed 4 years ago

cmnbroad commented 4 years ago

Prerequisite for https://github.com/broadinstitute/gatk/issues/6161.

codecov-io commented 4 years ago

Codecov Report

Merging #1430 into master will decrease coverage by 0.009%. The diff coverage is 72.549%.

@@              Coverage Diff               @@
##              master    #1430       +/-   ##
==============================================
- Coverage     68.359%   68.35%   -0.009%     
- Complexity      8486     8489        +3     
==============================================
  Files            583      583               
  Lines          34373    34389       +16     
  Branches        5730     5729        -1     
==============================================
+ Hits           23497    23505        +8     
- Misses          8655     8665       +10     
+ Partials        2221     2219        -2
Impacted Files Coverage Δ Complexity Δ
...c/main/java/htsjdk/tribble/index/IndexFactory.java 75.148% <72.549%> (-0.669%) 33 <14> (+5)
...tsjdk/tribble/index/linear/LinearIndexCreator.java 78.571% <0%> (-4.762%) 13% <0%> (-1%)
...k/tribble/index/interval/IntervalIndexCreator.java 84.906% <0%> (-3.774%) 13% <0%> (-1%)
...java/htsjdk/tribble/index/DynamicIndexCreator.java 76.563% <0%> (-3.125%) 13% <0%> (-1%)
src/main/java/htsjdk/samtools/BAMFileReader.java 68.466% <0%> (+0.852%) 52% <0%> (+1%) :arrow_up:
cmnbroad commented 4 years ago

@lbergelson I don't think the order in which we merge these matters, but we should probably wait for @jonn-smith 's redirect test before we merge either one.

lbergelson commented 4 years ago

Sorry, I merged mine which caused a conflict :(

lbergelson commented 4 years ago

@cmnbroad I merged the xsv fix.

cmnbroad commented 4 years ago

@lbergelson Rebased and conflicts resolved.