ReadAlignment.isBackExtension

Returns true iff the read alignment is an back extension, ie. it is an extension and reaches over the back of the reference contig.

1 Case 1 (complement alignment):
2 
3           0             ry lr
4     ref   |-->-->-->-+->-+--|
5                      | | |
6     read          |--+-<-+-<--<--<--|
7                   0     ay         la
8 
9 Case 2 (non-complement alignment):
10 
11           0             ry lr
12     ref   |-->-->-->-+->-+--|
13                      | | |
14     read          |--+->-+->-->-->--|
15                   0     ay         la