Linear Counts cross-reference in .bam

[xcwolfe]

I understand that DCC outputs both circ and linear counts for a given RNA strand. My question is specifically related to the linear counts - how is a count determined to be linear in DCC? What kind of filtering is applied that differentiates a linear count from a circular count? i.e., do reads with splice junctions or introns get reported as linear? What about reads that are soft-clipped, or reads with insertions or deletions?

Thanks,
Zach