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[nabis]
Fast hammer is a tool to calculate all pairwise hamming distances between words on a given list.
It will produce a distribution of the non-redundant hamming distances between all given words, as well as a file containing the minimum hamming distance between a given word and any other word on the list.
It is both multi-threaded and vectorized, so it's reasonably fast (though I'm sure it could be better).
make
./fastHammer testFile.txt 1
Example:
time ./fastHammer testFile.txt 1
Reading in barcodes from testFile.txt...
Num barcodes read in: 104
Computing hamming distances in 1 threads for barcodes of length: 16
Progress %:
10 20 30 40 50 60 70 80 90 100
........................................................................................................
# Hamming distance distribution:
0 20
1 32
2 0
3 0
4 0
5 0
6 0
7 0
8 0
9 0
10 0
11 0
12 0
13 0
14 0
15 64
16 5240
Writing per-barcode min hamming distance to: minimum_hamming_distances.tsv
DONE
real 0m0.010s
user 0m0.006s
sys 0m0.001s