CIGAR N operators (skips) are shown as N nucleotides and highlighted as variants

[peterjc]

Resurrecting an old issue for the GitHub issue tracker,

Given a CIGAR string like 50M561N26M with the N operator as used by BowTie/Cufflinks or TopHat to mark an intron, where the read skips a number of bases (here 561), Tablet v1.11.11.01 shows the read with a run of 516 N bases at this position (red letter N with a faded shading effect, as though it were a variant), giving the false impression that the raw read sequence included a lot of ambiguous bases.

I believe showing the skip as a run of pads/gaps (minus signs or asterisk depending on the user settings) as for a CIGAR D operator would be more intuitive. They should NOT be highlighted as variants.

Still occurs in Tablet v1.17.08.17, it does nicely highlight introns in RNA Seq mapping data (which may be useful if checking annotation, but is a distraction if SNP hunting), but the visual presentation in the main panel using red N's does still feel odd to me.