samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.
http://samtools.github.io/htsjdk/
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Removed redundant readability test in unrollPaths method #1355

Closed yfarjoun closed 5 years ago

yfarjoun commented 5 years ago

Cloud paths are slow to provide readability. This PR removes a readability check that comes right before opening a file. A failure to read the file will result in an error in both cases.

codecov-io commented 5 years ago

Codecov Report

Merging #1355 into master will increase coverage by 0.716%. The diff coverage is 25%.

@@               Coverage Diff               @@
##              master     #1355       +/-   ##
===============================================
+ Coverage     67.848%   68.564%   +0.716%     
- Complexity      8283      8805      +522     
===============================================
  Files            563       564        +1     
  Lines          33706     35024     +1318     
  Branches        5657      6012      +355     
===============================================
+ Hits           22869     24014     +1145     
- Misses          8659      8783      +124     
- Partials        2178      2227       +49
Impacted Files Coverage Δ Complexity Δ
src/main/java/htsjdk/samtools/util/IOUtil.java 58.111% <25%> (-0.101%) 118 <0> (ø)
...s/cram/encoding/external/ExternalLongEncoding.java 61.538% <0%> (-5.128%) 4% <0%> (+1%)
src/main/java/htsjdk/variant/bcf2/BCFVersion.java 93.103% <0%> (-1.633%) 12% <0%> (+5%)
src/main/java/htsjdk/samtools/SAMFileHeader.java 66.942% <0%> (-0.5%) 83% <0%> (+38%)
...dk/samtools/cram/structure/SubstitutionMatrix.java 91.026% <0%> (-0.279%) 30% <0%> (+15%)
...s/cram/encoding/external/ExternalByteEncoding.java 100% <0%> (ø) 10% <0%> (+4%) :arrow_up:
...ram/encoding/external/ExternalIntegerEncoding.java 100% <0%> (ø) 10% <0%> (+4%) :arrow_up:
...tools/cram/encoding/external/ExternalEncoding.java 100% <0%> (ø) 2% <0%> (?)
...c/main/java/htsjdk/samtools/util/IntervalList.java 73.913% <0%> (+0.016%) 103% <0%> (+34%) :arrow_up:
...n/java/htsjdk/samtools/cram/structure/SliceIO.java 84.524% <0%> (+1.19%) 15% <0%> (+1%) :arrow_up:
... and 17 more