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Add error output to VEP exceptions #5224

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merged 2 commits into from Feb 14, 2019

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tpoterba commented Jan 31, 2019

@cseed I have no idea if this will work.

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cseed left a comment

I have no idea, either. It looks no worse than the old code. Do we have a way to force VEP to generate an error?

I can't wait until this is handled by pipeline.


fatal(s"VEP command '${ cmd.mkString(" ") }' failed with non-zero exit status $rc\n" +
" VEP Error output:\n" +
Source.fromInputStream(new BufferedInputStream(proc.getErrorStream)).getLines().mkString("\n"))

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cseed Feb 8, 2019

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this should just be errorLines, no?

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tpoterba Feb 13, 2019

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yeah, oops.

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cseed approved these changes Feb 13, 2019

@danking danking merged commit 55ad895 into hail-is:master Feb 14, 2019

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