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Complement to the documentation

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Eric Coissac
2023-12-04 13:16:34 +01:00
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Release-notes.md
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## Latest changes
### Bug fixes
- In `obicsv` the **--keep count** was not equivalent to **--count**.
- In `obipairing` and `obipcrtag` correct a bug in the alignment procedure leading to negative scores.
- In `obimultiplex` correct a bug leading to a miss-read of the ngsfilter file when tags where written in lower case.
### New feature
- In `obimatrix` a **--transpose** option allows to transpose the produced matrix table in CSV format.
- In `obitpairing` and `obipcrtag` two new options **--exact-mode** and **--fast-absolute** to control the heuristic used in the alignment procedure. **--exact-mode** allows for disconnecting the heuristic and run the exact algorithm at the cost of a speed. **--fast-absolute** change the scoring schema of the heuristic.
- In `obitpairing` and `obipcrtag` two new options **--exact-mode** and **--fast-absolute** to control
the heuristic used in the alignment procedure. **--exact-mode** allows for disconnecting the heuristic
and run the exact algorithm at the cost of a speed. **--fast-absolute** change the scoring schema of
the heuristic.
- In `obiannotate` adds the possibility to annotate the first match of a pattern using the same algorithm
than the one used in `obipcr` and `obimultiplex`. For that four option were added :
- **--pattern** : to specify the pattern. It can use IUPAC codes and position with no error tolerated
has to be followed by a `#` character.
- **--pattern-name** : To specify the names of the slot used to report the results. Default is *pattern*
- **--pattern-error** : To specify the maximum number of error tolerated during matching process.
- **--allows-indels** : By default considered errors are mismatched, this flag allows for indels.
Only the first match is reported if several occurrences exist. If no match is found on direct strand then
pattern is looked for on the reverse complemented strand of the sequence.
### Enhancement
- For efficiency purposes, now the `obiuniq` command run on disk by default. Consequently, the **--on-disk** option has been replaced by **--in-memory** to ask explicitly to use memory.
### Bug fixes
- In `obicsv`, the **--keep count** was not equivalent to **--count**.
- In `obipairing` and `obipcrtag`, correct a bug in the alignment procedure leading to negative scores.
- In `obimultiplex`, correct a bug leading to a miss-read of the ngsfilter file when tags where written in lower case.
- In `obitag`, correct a bug leading to the annotation by taxid 1 (root) all the sequences having a 100% match
with one the reference sequence.
## November 16th, 2023. Release 4.1.0
### New feature