In the junctionCount code here, the first line of each input file is skipped. This results in one legitimate junction being dropped, at least as of regtools 0.5.1 in the example code cited here and shown here, as there is no header or other text in the first line of .count outputs from regtools that should be skipped. This also results in incorrect behavior when used in SPEAQeasy for the same reason.
The default behavior, at least when output='count', should be to not skip any lines.
In the
junctionCountcode here, the first line of each input file is skipped. This results in one legitimate junction being dropped, at least as of regtools 0.5.1 in the example code cited here and shown here, as there is no header or other text in the first line of.countoutputs from regtools that should be skipped. This also results in incorrect behavior when used in SPEAQeasy for the same reason.The default behavior, at least when
output='count', should be to not skip any lines.