Optimise sorting

[oameye]

The align_pair function in the sorting.jl file can be optimized in the following ways:

• Avoid unnecessary computations: You're computing the sortperm of the entire distances matrix, which is an O(n^2) operation. However, you only need the minimum distance for each reference, which can be found in O(n) time.

• Use efficient data structures: You're using arrays to keep track of which elements have been matched. Consider using a Set for this, which has O(1) lookup time.

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[jkosata]

Nice find! Has this part even been a bottleneck btw?

[oameye]

Yeah If I profilled this was the bottleneck but it seems that I am doing something wrong. The end result is not sorted properly. So I will have to look at it again anyway another time.