sgametrio / greedy-superstring

Find the shortest superstring of n strings in input from file

Greedy approximation algorithm to find shortest common superstring

Computational complexity

Given n reads of k max characters (k is hardcoded):

• overlap = O(k^2) -> overlap between 2 reads
• from_file = O(n*k) -> read input
• compute_lengths = O(n*k) -> count and save reads lenghts

Build the Dynamic Programming matrix [n, n] for overlaps costs overlap for every cell. So O(n^2*k^2).

Computing max n-1 times on the overlaps matrix costs O(n^3).

So total computational time is: O(n^2*k^2 + n^3).

Usage

Make it and run it passing as first argument the file containing input:

    make
    ./greedy-superstring <input_file>

As a working example, we include input.txt. Try running this:

    ./greedy-superstring input.txt

Output will be the shortest superstring found.

Input format

The file containing reads must be made of a # of lines without blank lines at the end.

Every line is read as a single string. Check input.txt as an example file