Computing the number of breakpoints

The number of breakpoints between a map (respectively a biological dataset marker ordering) and a reference order is computed by the mapbp (respectively dsbp) command. All the markers which do not appear in the reference order are not taken into account when computing the exact number of breakpoints. This number of breakpoints is the number of adjacent markers in an order which are not adjacent in the reference order. Two adjacent markers from two different chromosomes in the reference genome always count for one (obligate) breakpoint. For instance, the order ``1, 4, 3, 2, 5, 7, 6, 8, 9, 10'' has only three breakpoints with the reference order ``(chr01)1,2,3,4,5,8,(chr02)9,10'': the breakpoints are 1-4, 2-5, and 8-9 (they are not on the same chromosome in the reference genome). 5-7 and 6-8 are not breakpoints because markers 6 and 7 do not appear in the reference order.

Thomas Schiex 2009-10-27