RSeqC and bwa-mem

[long le]

We have targeted RNA-Seq data mapped with the latest bwa-mem.  How does RSeqC treat chimeric alignments which show a primary alignment and a supplementary alignment which both could be from two exons in one gene or two exons in two different genes?  Does each alignment get tagged separately or is one of the two (primary only, perhaps) chosen for tagging?

Thanks,

Long