global alignment

[Lioscro]

Global alignment implementation (#127, #136, #139)

• Added a method argument to pp.align_sequences which can either be local (default) or global.
• Moved alignment functions to pp.alignment_utilities.
• Bumped some dependencies that were required.
• The gap open and gap extend penalties were left as is (20 and 1 respectively). Turns out this matches exactly to the values used in the original GESTALT paper (10 and 0.5; multiplicatively identical).

Regarding poly-A trimming, I'm not sure if this will be a big issue, but worth discussion.

[codecov[bot]]

Codecov Report

Merging #142 (6d5230e) into master (3b454a7) will increase coverage by 0.44%. The diff coverage is 89.28%.

@@            Coverage Diff             @@
##           master     #142      +/-   ##
==========================================
+ Coverage   86.23%   86.67%   +0.44%     
==========================================
  Files          65       65              
  Lines        4532     4540       +8     
==========================================
+ Hits         3908     3935      +27     
+ Misses        624      605      -19     

Impacted Files	Coverage Δ
cassiopeia/preprocess/constants.py	100.00% <ø> (ø)
cassiopeia/preprocess/pipeline.py	75.93% <82.35%> (+4.92%)	:arrow_up:
cassiopeia/preprocess/alignment_utilities.py	90.00% <100.00%> (+1.25%)	:arrow_up:

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