Open IanSudbery opened 5 years ago
bam2bam throws an error if the log files is not redirected, but the output is sent to stdout.
bam2bam
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
cgatflow.cgatpipelines.tasks.addPseudoSequenceQuality
Should probably throw an error if log is not redictered and verbosity > 0
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