Optimize Permuter for small Reads

[Parvfect]

Currently biggest bottleneck in the pipeline - needs fixing

[Parvfect]

Looks like Permuter is wrong according to Roman

[Parvfect]

Need a fresh perspective - leaving for training - will do this later

[Parvfect]

Fixed the method now based on growing partial sum. Actually gotta read for smaller reads, however iterations are really really small. Current code looks like this, needs to be optimized.

def permuter1(arr, ffield):

    possibilities = set(arr[0])
    new_possibilities = set()
    counter = 1
    for i in range(1, len(arr)):
        for k in possibilities:
            for j in arr[i]:
                new_possibilities.add(j+k)
        possibilities = new_possibilities 
        new_possibilities = set()

    return set([-(i %ffield) %ffield for i in possibilities])

[Parvfect]

[Parvfect]

Works for small Reads, but still disgustingly slow, since the number of possibilites explode. Would love to somehow make it faster. If I can, I'll do it. If not, well - we have to let it go. It does work now.

[Parvfect]

Done