An enhancement on the GUI for TagPileup (Read Analysis). As we build out new features on Tag Pileup and the parameter selection becomes more complex, a visual/graphical guide to selecting parameters would be valuable for user clarity.
Using the Graphics objects, draw a cartoon of a sequence read fragment with a "Read 1" and a "Read2" within the TagPileupWindow object. An arrow should point to the 5' End of Read 1 to start (reflect default parameters) and update to move the arrow/add new arrows at the points where the aligned fragment will be marked/counted on the genome position tallies.