Creating this as a separate issue so it's easy to track when it's done. Here's the original post from a probably related issue:
@Kuanhao-Chao, I guess this is something we hadn't considered (i.e. double counting).
Whether or not double counting is the issue in this case, we should add a test where double counting occurs. We should then add a check when parsing regular expressions that each read is assigned to one and only one group (e.g. Forward, reverse, or the contig groups). In the case that 1 or more reads could be assigned to >1 group, we should spit an Error with an error message that tablutes for each such read all the groups that it has been assigned to, as well as the suggestion that users can use a CSV file (with a link to the documentation for how to do it) if the regular expressions are not working.
Creating this as a separate issue so it's easy to track when it's done. Here's the original post from a probably related issue:
@Kuanhao-Chao, I guess this is something we hadn't considered (i.e. double counting).
Whether or not double counting is the issue in this case, we should add a test where double counting occurs. We should then add a check when parsing regular expressions that each read is assigned to one and only one group (e.g. Forward, reverse, or the contig groups). In the case that 1 or more reads could be assigned to >1 group, we should spit an Error with an error message that tablutes for each such read all the groups that it has been assigned to, as well as the suggestion that users can use a CSV file (with a link to the documentation for how to do it) if the regular expressions are not working.
Originally posted by @roblanf in https://github.com/roblanf/sangeranalyseR/issues/53#issuecomment-765021128