Add optional reference FASTA for non-SARS-CoV-2 genomes#614
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Add optional reference FASTA for non-SARS-CoV-2 genomes#614jeromekelleher wants to merge 1 commit into
jeromekelleher wants to merge 1 commit into
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Make the reference genome an optional input so inference can run on genomes other than SARS-CoV-2, as a non-breaking change: all new parameters default to the built-in SARS-CoV-2 reference. - import-alignments gains a --reference option, sizing/labelling the dataset from the supplied FASTA (Dataset.new gains sequence_length and contig_id kwargs). - infer reads an optional reference_fasta config key, threaded through initial_ts; genome length and identity metadata are derived from the FASTA and the length is checked against the dataset contig length. - match_path_ts takes the sequence length from the working tree sequence rather than the hardcoded constant. - Non-SARS-CoV-2 runs use a generic time-zero epoch for the reference.
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #614 +/- ##
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+ Coverage 88.07% 88.18% +0.11%
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Files 12 12
Lines 4134 4165 +31
Branches 585 593 +8
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+ Hits 3641 3673 +32
Misses 365 365
+ Partials 128 127 -1
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WIP I need to look through this properly |
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Make the reference genome an optional input so inference can run on genomes other than SARS-CoV-2, as a non-breaking change: all new parameters default to the built-in SARS-CoV-2 reference.
Closes #609