Fig. 1.

Definition of local inversions. The red segment (L, R) in the reference is a local inversion if it is reverse complemented (as in the figure), and the four indicator segments of length δ are only subject to small variations/indels. Two reads A and B must be split and aligned (in pair) in different orientations to the reference in the manner exactly as shown here, where the dashed lines indicate the ordering of the split reads. These split alignments covering the four δ segments guarantee that the four δ segments do not change substantially.