Reference-less contig stitching

[Donaim]

No description provided.

[codecov]

Codecov Report

❌ Patch coverage is 73.91304% with 12 lines in your changes missing coverage. Please review.
✅ Project coverage is 86.48%. Comparing base (99412d5) to head (aebd00f).
⚠️ Report is 18 commits behind head on master.

Files with missing lines	Patch %	Lines
micall/core/contig_stitcher.py	70.00%	12 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1221      +/-   ##
==========================================
- Coverage   87.14%   86.48%   -0.66%     
==========================================
  Files          31       31              
  Lines        7545     7223     -322     
==========================================
- Hits         6575     6247     -328     
- Misses        970      976       +6     

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[Donaim]

So I'm working on optimizing the stitcher.
The current profiling looks like this:

Evidently, fractions are very slow

[Donaim]

This is the same profiling results, after fractions have been replaced by ints: