Adamtaranto
commented
6 years ago teloclip commit 23116e996faad3b3a28ac245f93146366c54d046 requires motif matches to occur in clipped region of a read overhanging a contig end.
- Internal clips are ignored
- Matches may occur in either end of an alignment that overhangs both ends of a contig
Motif search currently requires at least one instance of any user-specified motif in a read that is clipped at a contig end. This match can occur anywhere in the read, and may not necessarily be in the distal clipped region.
Add option to restrict motif search to the clipped end (or ends for long reads that span entire contigs).