In some cases, users can have paired reads that have the same exact name, without any suffix like /1 or /2. If those same-name reads are given as input to MATAM/SortMeRNA, the resulting alignments will be undistinguishable, causing unforeseen (and probably bad) consequences when building and compressing the overlap graph.
Since it would be very difficult to check that such reads exist in the input file, we need to at least add a warning in the README/manual, so that users know they need to have a unique name for every read. This warning could also include advice on adding suffixes like /1 or /2 to paired-end reads that would have the same name.
In some cases, users can have paired reads that have the same exact name, without any suffix like
/1or/2. If those same-name reads are given as input to MATAM/SortMeRNA, the resulting alignments will be undistinguishable, causing unforeseen (and probably bad) consequences when building and compressing the overlap graph.Since it would be very difficult to check that such reads exist in the input file, we need to at least add a warning in the README/manual, so that users know they need to have a unique name for every read. This warning could also include advice on adding suffixes like
/1or/2to paired-end reads that would have the same name.