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adding new overloads to IOUtils with Path for some file only methods #1296

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merged 4 commits into from
Feb 21, 2019
Merged

adding new overloads to IOUtils with Path for some file only methods #1296

merged 4 commits into from
Feb 21, 2019

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lbergelson
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Description

Add Path overloads of some functions in IOUtil that were missing them.
Fixes #1294

Checklist

  • Code compiles correctly
  • New tests covering changes and new functionality
  • All tests passing
  • Extended the README / documentation, if necessary
  • Is not backward compatible (breaks binary or source compatibility)

This was referenced Feb 20, 2019
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codecov-io commented Feb 20, 2019 •
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Codecov Report

Merging #1296 into master will increase coverage by 0.234%.
The diff coverage is 61.538%.

@@               Coverage Diff               @@
##              master     #1296       +/-   ##
===============================================
+ Coverage     67.508%   67.742%   +0.234%     
- Complexity      8148      8332      +184     
===============================================
  Files            557       560        +3     
  Lines          33384     33883      +499     
  Branches        5631      5751      +120     
===============================================
+ Hits           22537     22953      +416     
- Misses          8662      8727       +65     
- Partials        2185      2203       +18
Impacted Files Coverage Δ Complexity Δ
src/main/java/htsjdk/samtools/util/IOUtil.java 57.606% <61.538%> (+0.463%) 118 <11> (+3) ⬆️
...samtools/util/AsyncBlockCompressedInputStream.java 72% <0%> (-4%) 12% <0%> (-1%)
...ava/htsjdk/samtools/CRAMContainerStreamWriter.java 70.612% <0%> (-0.289%) 54% <0%> (ø)
...dk/samtools/util/IntervalCoordinateComparator.java 58.333% <0%> (ø) 6% <0%> (?)
.../main/java/htsjdk/samtools/util/IntervalCodec.java 79.412% <0%> (ø) 8% <0%> (?)
.../java/htsjdk/samtools/util/IntervalListWriter.java 88% <0%> (ø) 5% <0%> (?)
...rc/main/java/htsjdk/samtools/util/BinaryCodec.java 70.183% <0%> (+0.459%) 57% <0%> (+1%) ⬆️
src/main/java/htsjdk/samtools/BAMFileReader.java 68.665% <0%> (+0.817%) 52% <0%> (+1%) ⬆️
src/main/java/htsjdk/samtools/util/Interval.java 63.636% <0%> (+1.818%) 26% <0%> (+1%) ⬆️
src/main/java/htsjdk/samtools/util/StringUtil.java 70.936% <0%> (+1.97%) 73% <0%> (+2%) ⬆️
... and 4 more

@lbergelson lbergelson mentioned this pull request Feb 20, 2019
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yfarjoun
yfarjoun reviewed Feb 21, 2019
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src/main/java/htsjdk/samtools/util/IOUtil.java Outdated Show resolved Hide resolved
src/test/java/htsjdk/samtools/util/IOUtilTest.java Outdated
try( final Writer out = IOUtil.openFileForBufferedWriting(tmp)){
out.write(expected);
}
try( final BufferedReader in = IOUtil.openFileForBufferedReading(tmp)){
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can you somehow check that the zipped files are really zipped and that the plaintext ones are really plaintext?

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done

Yossi Farjoun and others added 2 commits February 21, 2019 14:09
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@yfarjoun I responded to your comments, good to go?

yfarjoun
yfarjoun reviewed Feb 21, 2019
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no need for final in TWR..also spaces

src/test/java/htsjdk/samtools/util/IOUtilTest.java Outdated Show resolved Hide resolved
src/test/java/htsjdk/samtools/util/IOUtilTest.java Outdated Show resolved Hide resolved
src/test/java/htsjdk/samtools/util/IOUtilTest.java Outdated Show resolved Hide resolved
@lbergelson
Apply suggestions from code review
0ad3238 
change spaces

Co-Authored-By: lbergelson <[email protected]>
@lbergelson lbergelson merged commit 3b3d107 into master Feb 21, 2019
@lbergelson lbergelson deleted the lb_more_path_methods_ioutil branch February 21, 2019 21:59
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@lbergelson @codecov-io @yfarjoun