[vcf] replace augur's read_vcf with TreeTime's #1366
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #1366 +/- ##
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- Coverage 66.68% 66.65% -0.03%
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Files 69 69
Lines 7330 7321 -9
Branches 1801 1799 -2
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- Hits 4888 4880 -8
Misses 2172 2172
+ Partials 270 269 -1 ☔ View full report in Codecov by Sentry. |
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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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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_vcffunction (which has moved around quite a lot) was first introduced by 278a30e in May2018. 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