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docs: add min match rate to changelog
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ivan-aksamentov committed Jun 24, 2022
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4 changes: 3 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -27,6 +27,8 @@ Also, it is now much simpler to contribute to Nextclade. If you wanted to contri

- "Terminal band width" controls the extra band width that is necessary for correct alignment if terminal indels occur.

- **Feature**: "Min match rate" parameter is added, which sets required rage of seed matches in a sequence (number of matched seeds divided by total number of attempted seeds). If the measured rate is below required, alignment will not be attempted, as for such sequences, there is a high chance of infeasible memory and computational requirements. The default value is 0.3.

- **Fix**: 3' terminal insertions are now properly detected

### Genes on reverse (negative) strand
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- The new flag `--output-translations` is a dedicated flag to provide a file path template which will be used to output translated gene fasta files. This flag accepts a template string with a template variable `{{gene}}`, which will be substituted with a gene name. Each gene therefore receives it's own path. Additionally, the translations are now independent from output directory and can be omitted if they are not necessary.

- **Feature**: `--excess-bandwidth` and `--terminal-bandwidth` arguments are added (see "Alignment algorithm rewritten with adaptive bands" section for details)
- **Feature**: New `--excess-bandwidth`, `--terminal-bandwidth`, `--min-match-rate` arguments are added (see "Alignment algorithm rewritten with adaptive bands" section for details)

Example:

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