re-enable reading bam files from pipes #1085
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Codecov Report
@@ Coverage Diff @@
## master #1085 +/- ##
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+ Coverage 66.179% 66.183% +0.004%
Complexity 7635 7635
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Files 535 535
Lines 32394 32401 +7
Branches 5510 5512 +2
===============================================
+ Hits 21438 21444 +6
- Misses 8790 8792 +2
+ Partials 2166 2165 -1
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jacarey
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Feb 8, 2018
| @@ -335,7 +347,7 @@ public URL asUrl() { | |||
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| @Override | |||
| public SeekableStream asUnbufferedSeekableStream() { | |||
| return lazySeekableStream.get(); | |||
| return lazySeekableStream.get(); | |||
jacarey
reviewed
Feb 8, 2018
| } | ||
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| @Override | ||
| public InputStream asUnbufferedInputStream() { | ||
| return asUnbufferedSeekableStream(); | ||
| final SeekableStream seekableStream = asUnbufferedSeekableStream(); | ||
| if( seekableStream != null) { |
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space after if and not before seekableStream
jacarey
reviewed
Feb 8, 2018
| return lazySeekableStream.get(); | ||
| //if the file doesn't exist, the try to open the stream anyway because users might be expecting the exception | ||
| //if it not a regular file than we won't be able to seek on it, so return null | ||
| if(!fileResource.exists() || fileResource.isFile()) { |
jacarey
approved these changes
Feb 8, 2018
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fixing an issue that prevented reading a bam file from an unseekable file, ex: a unix pipe
fixes #1083 which was introduced by #1077
this only fixes the case where the bam is being opened as file, a similar issue exists for Paths, #1084
support for reading pipes as paths has never worked
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