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Use usher-sampled if installed#499

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AngieHinrichs merged 3 commits intocov-lineages:mastercov-lineages/pangolin:masterfrom AngieHinrichs:usher-sampledAngieHinrichs/pangolin:usher-sampledCopy head branch name to clipboardJan 3, 2023

+12-1

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Commits on Dec 9, 2022

• Use the much faster usher-sampled if it is installed; otherwise, print out a message recommending that the user update usher. Include the usher(-sampled) command in the log output to help with debu…

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Commits on Dec 14, 2022

• Improvements to info messages suggested by @aineniamh in PR cov-lineages#499 code review

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Commits on Jan 3, 2023

• Remove message about usher 0.6.1 not available on Mac because bioconda has it now.

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