Add aln2counts_simplify tool

[Donaim]

This is similar to denovo_simplify,
but only runs the postprocessing part.

[codecov]

Codecov Report

All modified lines are covered by tests ✅

Comparison is base (3f791c5) 86.43% compared to head (89bc579) 86.43%.

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1023   +/-   ##
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  Coverage   86.43%   86.43%           
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  Files          28       28           
  Lines        6110     6110           
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  Hits         5281     5281           
  Misses        829      829           

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[donkirkby]

Two very minor suggestions, but it looks good to me.

Does it work?

[Donaim]

@donkirkby It worked for a smaller example, but I have not yet confirmed it for a bigger test.
The final version of stitched.csv does not seem to contain the searched sequence, even though I am directly asserting that it does in the test.
Maybe it's because that final version is supposed to fail the test actually.

[Donaim]

Update: it works. @donkirkby

[donkirkby]

A couple of minor simplifications to consider.