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Centralize sequence read operations #1730

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Centralize sequence read operations #1730

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@victorlin victorlin commented Jan 17, 2025 •
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Description of proposed changes

General improvements before fixing CI failures related to sequence read.

Related issue(s)

#1727

Checklist

@victorlin
Replace usage of Bio.SeqIO.parse with read_sequences
aa0939d 
This centralizes customization of the Biopython call.
@victorlin
Add types for augur.io.read_sequences
b013372
@victorlin
Add alias to Bio.SeqIO.read
d9e977e 
This allows for centralized customization of the Biopython call.
@victorlin
Replace usage of Bio.SeqIO.read with read_sequence
63cdf89 
This centralizes customization of the Biopython call.
@victorlin victorlin self-assigned this Jan 17, 2025
@victorlin victorlin mentioned this pull request Jan 17, 2025
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@victorlin victorlin marked this pull request as ready for review January 17, 2025 23:26
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