Returns true if the aligned read contigB (with extensions on either end) is fully contained in the reference contigA.
According to the following 'definition' contigA is fully contained in contigB iff x >= 0 and y <= l_a.
1 0 x ua va y la 2 contigA |------------------+---+-+---+-+---+-------------------------| 3 / / / | | | \ \ \ 4 / / / | | | \ \ \ 5 / / / | | | \ \ \ 6 / / / | | | \ \ \ 7 contigB |---+------+---+------+---| 8 0 ub vb lb 9 10 x = ua - (ub - 0) = ua - ub 11 y = va + (lb - vb)
See Implementation
Returns true if the aligned read contigB (with extensions on either end) is fully contained in the reference contigA.
According to the following 'definition' contigA is fully contained in contigB iff x >= 0 and y <= l_a.