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add the --skip-empty option

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Former-commit-id: ec9cb0ecaf90a61bf9289cf4c089b5cc2fcb65a5
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Eric Coissac
2023-07-17 14:24:02 +02:00
parent b44fcfb2a0
commit be47ec909c
10 changed files with 65 additions and 12 deletions
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Release-notes.md
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@ -4,7 +4,9 @@
### Bugs
- Patch a bug in the install script for correctly follow download redirection.
- Patch a bug in the install-script for correctly follow download redirection.
- Patch a bug in `obitagpcr` to consider the renaming of the `forward_mismatch` and `reverse_mismatch` tags
to `forward_error` and `reverse_error`.
### Enhancement
@ -14,6 +16,10 @@
### New feature
- In every *OBITools*, writing an empty sequence (sequence of length equal to zero) through an error and
stops the execution of the tool, except if the **--skip-empty** option is set. In that case, the empty
sequence is ignored and not printed to the output. When output involved paired sequence the **--skip-empty**
option is ignored.
- In `obiannotate` adds the **--set-identifier** option to edit the sequence identifier
- In `obitag` adds the **--save-db** option allowing at the end of the run of `obitag` to save a
modified version of the reference database containing the computed index. This allows next