ls11-www.cs.tu-dortmund.de/_media/staff/kopczyns/meds-for-bs.pdf
0, 0, 0, 1, 2, 3, 3, 3, 4 C 5 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2 G 7 0, 0, 0, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3 T 10 1, 2, 2, 2, 3, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5
Tbwt = T T C G T T G T $ A A [...] Typically the register size (long int) r = 64 is suitable.
c occ[c]
A 0, 0, 3 C 1, 1, 1 G 1, 2, 2 T 2, 5, 5
Tbwt = T T C G T T G T $ A A A C G A
(Example: r = 4)
Determination of new interval •Given: interval [...] 2 if L > 0: 3 block_l = (L - 1) >> 6 4 appear_l = popcnt(app[c][block_l] << (63 - ((L - 1) & 63))) 5 appear_r = popcnt(app[c][block_r] << (63 - (R & 63))) 6 if block_l > 0: occur_l = occ[c][block_l - 1] …