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bam2bam and log redirection #30

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IanSudbery opened this issue Oct 23, 2018 · 0 comments
Open

bam2bam and log redirection #30

IanSudbery opened this issue Oct 23, 2018 · 0 comments

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@IanSudbery
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bam2bam throws an error if the log files is not redirected, but the output is sent to stdout.

This is presumably because a bam file with a log in the front is not a valid bam.

However, this happens even if the log level is set to 0.

This is how bam2bam is used in cgatflow.cgatpipelines.tasks.addPseudoSequenceQuality

Should probably throw an error if log is not redictered and verbosity > 0
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@IanSudbery