####################### ####### Rules ######### ####################### - All Projects will be implemented in C++. ###################### #### 1st project ##### ###################### Task for the first project: - map reads with semi-global alignment (with windowing technique?) on large string - implement Ukkonen trick - compare standard vs Ukkonen vs razers3 What we have: ------------- - FASTA files - Genome (1 file) - Lots of reads - Read in Genome - Reads as vectors What we do: ------------ - Smith Waterman semi-global alignment (modified) - Using linear space (not having the whole matrix but only a part of it) -- Need to figure out a way to do the backtracking!!! - Using Ukkonen trick - Using RazerS (as comparison) (we need the runtime) - Tips (Sandro): --------------- - Avoid pointers where possible, use references (call by reference: T&ref) - Only read string, do not write! - creating dynamic programming matrix: more dimensional arrays in C++.. not helping => dynamic arrays - use this: vector<vector<int>> with constructor (La, vector<int>(Lb)) can be accessed with blub[i][j]