In https://github.com/fulcrumgenomics/prymer/blob/main/prymer/offtarget/offtarget_detector.py the OffTargetDetector (and bwa), when we search for off-targets for a primer or primer-pair, we always return the on-target (where the primer/primer-pair was designed). Do we want to filter the expected location out if we're calling this "off-target detector"?
Also, when bwa finds many many hits, it may not return the mappings of any hit, or just one representative hit. In both cases we get the count of off-targets. When this happens, the on-target mapping may not be returned. Do we want to change the behavior at all in either case?
In
https://github.com/fulcrumgenomics/prymer/blob/main/prymer/offtarget/offtarget_detector.pytheOffTargetDetector(andbwa), when we search for off-targets for a primer or primer-pair, we always return the on-target (where the primer/primer-pair was designed). Do we want to filter the expected location out if we're calling this "off-target detector"?Also, when
bwafinds many many hits, it may not return the mappings of any hit, or just one representative hit. In both cases we get the count of off-targets. When this happens, the on-target mapping may not be returned. Do we want to change the behavior at all in either case?