Definition 2 (Read Assignment): a read belongs to an edge $$e=(tail,head,mode,T)$$ iff each two bases contiguously aligned to the genome $$G[i]G[i+1]$$ map to adjacent RNA-coordinates $$R[j]R[j+1]$$ within e: $$tail_e \leq j < j+1 \leq head_e$$.
Reads can naturally overlap one or multiple adjacent exonic segments $$\left<e,\ldots,e_n\right>$$, i.e. to edges $$e_i$$ such that $$mode_{e_i}=exonic$$. To this end we extend E by corresponding super-edges se conflating the attributes of atomary exon segments, $$se=(tail_e, head_{e_n}, exonic, \bigcap T_{\{e,...,e_n\}})$$ and apply Definition 2 without loss of generality. Note that in the case of split-mappings, exonic segments represented by super-edges can be separated by intermediate intronic edges. Paired-end reads are mapped jointly to super-edges that combine the exonic regions to which each mate is mapping, which in turn can be already super-edges (Fig.2).