2.0.0-beta.7
Pre-release
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Commit history
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- [
a2f174d] feat(cli): allow to replace unknown nucs with Ns
This adds a flag --replace-unknown to run command, which allows to replace unknown nucleotide characters with 'N'.
By default, the sequences containing unknown nucleotide nucleotide characters are skipped with a warning - they
are not aligned and not included into results. If this flag is provided, then before the alignment,
all unknown characters are replaced with 'N'. This replacement allows to align and analyze these sequences.
The following characters are considered known:
-ABCDGHKMNRSTVWY
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cae1f51] Merge remote-tracking branch 'origin/master' into feat/cli-replace-unknown -
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d8f5f28] feat(cli): organize verbosity flags towards the end of help message
Currently --verbosity, --silent, -v and -q args are missorted in the --help message text.
Here I inline the clap-verbosity-flag crate (only 1 file) and modify it, adding our custom flags and display_order annotations, such that the args are shown in the very end of the message, just before the --help arg.
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d98312a] Merge pull request #883 from nextstrain/feat/cli-organize-verbosity-flags -
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fc4c089] feat(cli): add headings for help sections
There are many arguments for run command, so let's organize them in named sections.
It required splitting args into separate structs and adding next_help_heading annotations.
I could not figure out how to change the "OPTIONS" heading where the default --help arguments stays. So I added a fake indentation for all heading as if they are nested under "OPTIONS".
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a1ff027] Merge pull request #884 from nextstrain/feat/cli-add-help-headings -
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1aa6b0f] feat: add minimum seed matching rate -
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d437b49] Merge pull request #885 from nextstrain/fix/avoid-large-allocations
fix: avoid large allocations during alignment