incorporate htsjdk 2.13.1 #1007
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this includes a critical fix for every tool that uses a sorting collection
lbergelson
referenced
this pull request
in samtools/htsjdk
Dec 1, 2017
* fixing the crash on shutdown introduced in #910 by changing the command that gets run on on deleteOnExit Files.delete() -> Files.deleteIfExists() this will prevent the jvm from crashing on shutdown if the temporary files get cleaned up before it closes * This still leaves open the possibilty of crash on shutdown if the temporary file is unable to be removed for some other reason. That's subtly different than the File version of deleteOnExit, but it may be useful to get these error messages in the unusual case of failing to delete a file that exists. * fixes #1029
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yfarjoun
approved these changes
Dec 12, 2017
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this includes a critical fix for every tool that uses a sorting collection
see https://github.com/samtools/htsjdk/releases/tag/2.13.1
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