Make sure reference accessions are for the right segment

[priyappillai]

Currently, when automatically getting the reference sequences, ADAPT does not check for which segment the reference sequences are for. This does not cause any errors, as reference sequences for the wrong segment will be removed during the alignment process, but it does mean that curation will not curate out any sequences that have a mislabeled segment in NCBI's database. This PR adds a check while getting reference sequences to make sure they are for the correct segment.

adapt/prepare/ncbi_neighbors

• Add segment as input to construct_references and filter for segment using source features
• Make parse_genbank_xml_for_source_features output a dictionary for source features

bin/design.py

• Add segment as input to construct_references

[codecov[bot]]

Codecov Report

Merging #61 (bbbf444) into main (6527d50) will decrease coverage by 0.07%. The diff coverage is 36.84%.

@@            Coverage Diff             @@
##             main      #61      +/-   ##
==========================================
- Coverage   86.30%   86.22%   -0.08%     
==========================================
  Files          50       50              
  Lines        8219     8227       +8     
==========================================
+ Hits         7093     7094       +1     
- Misses       1126     1133       +7     

Impacted Files	Coverage Δ
adapt/prepare/ncbi_neighbors.py	42.75% <33.33%> (-0.59%)	:arrow_down:
bin/design.py	65.81% <100.00%> (ø)

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