disregard non productive contigs when reporting chain/locus status

[zktuong]

@suochenqu requested to change the locus/chain status to mainly reflect only productive contigs.

This is now the default behaviour, but can be toggled with report_status_productive=True or report_status_productive=False with ddl.Dandelion.

for some context:

there are extra contigs in the J only TRA and TRB
there's no term at the moment for describing this combination other that extra pair and it's not technically a single pair either
it's orphan VDJ if we consider only productive contigs.

chain_status depends on locus_status -> which currently says Extra VDJ + TRA -> this only checks at the locus column for how many TRB and TRA contigs there are. if chain_status detects the word Extra (and in this case there are 2 TRB VDJ contigs, hence extra VDJ), it will then just simply flag this as an Extra pair

[zktuong]

isotype status is still being reflected as Multi - so still need some more fixes.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 83.75%. Comparing base (6998cc6) to head (5147c22).
Report is 7 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #366      +/-   ##
==========================================
+ Coverage   83.73%   83.75%   +0.01%     
==========================================
  Files          52       52              
  Lines        9070     9080      +10     
==========================================
+ Hits         7595     7605      +10     
  Misses       1475     1475              

Flag	Coverage Δ
unittests	83.75% <100.00%> (+0.01%)	⬆️

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Files	Coverage Δ
dandelion/utilities/_core.py	87.81% <100.00%> (+0.03%)	⬆️
dandelion/utilities/_utilities.py	83.80% <100.00%> (+0.16%)	⬆️
tests/test_io.py	100.00% <100.00%> (ø)