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cgat-apps repository
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bam2bam and log redirection #30

Open IanSudbery opened 5 years ago

IanSudbery commented 5 years ago

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