ls11-www.cs.tu-dortmund.de/_media/staff/kopczyns/meds-for-bs.pdf
index d
c less[c] occ[c]
A 1 0, 0, 0, 0, 0, 0, 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 [...] most 1. Store information where character appears bitwise in app table.
c app[c]
A 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 1 C 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0 G 0, 0, 0, 1, 0, 0, 1, 0, 0 [...] 0, 0, 0, 0, 0, 1, 0 T 1, 1, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0
Tbwt = T T C G T T G T $ A A A C G A
Bits are stored in blocks of long int type. Trick: using hardware implemented command popcnt to count …