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SplitBamByCell doesn't validate outputs early enough #226

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jamesnemesh opened this issue Jan 24, 2021 · 0 comments
Open
1 task done

SplitBamByCell doesn't validate outputs early enough #226

jamesnemesh opened this issue Jan 24, 2021 · 0 comments

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@jamesnemesh
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Instructions

Run SplitBamByCell but specify OUTPUT_LIST or REPORT parameter where the program does not have write access.
Program can have significant run time, only to fail at the end of the process with
Exception in thread "main" htsjdk.samtools.SAMException: Error opening file for writing

Affected tool(s)

SplitBamByCell

Affected version(s)

  • Latest public release version [version?]

Expected behavior

SplitBamByCell should use IOUtil.assertFileIsWritable to validate all outputs before starting process.

Actual behavior

SplitBamByCell runs until finished, then fails to write files due to path or permissions issues.

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