[vcf] replace VCF reading with TreeTime's read_vcf
#1357
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jameshadfield
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Dec 20, 2023
The strain names are available from TreeTime's function of the same name. This function is preferable to (a) reduce duplicated logic and (b) because it performs more thorough validation of the VCF file. Aside: Augur's `read_vcf` function (which has moved around quite a lot) was first introduced by 278a30e in May 2018. This returned a tuple of `(strain_names, strain_names.copy())` and this return signature has been kept during refactors despite us having since stopped using the second argument, except for in tests! Closes #1357
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jameshadfield
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Jan 24, 2024
The strain names are available from TreeTime's function of the same name. This function is preferable to (a) reduce duplicated logic and (b) because it performs more thorough validation of the VCF file. Aside: Augur's `read_vcf` function (which has moved around quite a lot) was first introduced by 278a30e in May 2018. This returned a tuple of `(strain_names, strain_names.copy())` and this return signature has been kept during refactors despite us having since stopped using the second argument, except for in tests! Closes #1357
jameshadfield
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Jan 25, 2024
The strain names are available from TreeTime's function of the same name. This function is preferable to (a) reduce duplicated logic and (b) because it performs more thorough validation of the VCF file. Aside: Augur's `read_vcf` function (which has moved around quite a lot) was first introduced by 278a30e in May 2018. This returned a tuple of `(strain_names, strain_names.copy())` and this return signature has been kept during refactors despite us having since stopped using the second argument, except for in tests! Closes #1357
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(I'm going to re-open this issue and generalise it.) |
jameshadfield
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read_vcf with TreeTime'sread_vcf
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Augur uses a variety of functions to read VCF files, including TreeTime's
read_vcfwhich now includes a lot of validation and helpful error messages. We should shift all our VCF reading to use this function.augur maskAugur mask uses a function
get_chrom_name(vcf_file)to read (part of) the VCF file. See #507 for more context.augur sequence-traitsdefines its own
read_in_translate_vcffunction, but see this comment for context.augur.io.vcfUpdate: removed in #1366
augur.io.vcfincludesread_vcfwhich is (only) used byaugur index. It's a bit of a misnomer as it actually only returns the strain names (from the VCF header). The treetime functionread_vcfis a more thorough function as it (now) checks the validity of the VCF file, however it doesn't actually return a list of the strain names. It could very easily be extended to do so, and then I think we should replace Augur's function with TreeTime's.(TreeTime's function will be slower because it parses the entire VCF, but (a) I think this difference will be negligible and (b) this will flag up errors in the VCF data lines which I think is appropriate.)
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