2.0.0-beta.9
Pre-release
| This is a pre-release. It can contain bugs and significant changes which are not yet finalized. Changes may appear without notice. We recommend to try the pre-releases to learn about upcoming features. For important projects, use stable releases. |
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Commit history
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- [
bc9839c] feat: retry with reverse complement when seed matching fails
Adds flag --retry-reverse-complement which enables additional attempt of seed matching when initial attempt fails. The second attempt is performed on reverse-complemented sequence.
As a consequence, the output alignment, peptides and analysis results correspond to this modified sequence and not to the original.
This functionality is opt-in and the default behavior is to skip sequence with a warning.
-
[
879f780] feat: append suffix to sequence if reverse complemented -
[
fa8f275] feat(cli): issue a warning when a sequence was reverse-complemented -
[
fb271be] Merge remote-tracking branch 'origin/master' into feat/reverse-if-seed-fails -
[
2605cca] feat: add warning to errors.csv when sequence gets reverse-complemented -
[
18bdc94] feat: add "isReverseComplement" columt to csv and tsv outputs -
[
7316d01] feat(cli): default basename to a consistent hardcoded value
Currently, if --output-basename is not provided, and the basename for files written to --output-all is the same is for input fasta. However, if multiple fasta files provided, it switches to a hardcoded "nextaclade" or "nextalign".
This is not something that other CLI tools typically do and might be confusing, especially for use-cases where a certain filename is expected (i.e. in scripts and pipelines), especially when a number of input fasta files is not known in advance or if it changes between 2 runs.
This PR proposes to always use a hardcoded name for consistency, so that there is no surprise.