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Bug in the json parsing

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Eric Coissac
2024-03-19 13:50:13 +01:00
parent 11a14b6dc8
commit e25c3b7365
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Release-notes.md
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## Latest changes
### New feature
- A new OBITools named `obiscript` allows to process each sequence according to a Lua script. This is
an experimental tool. The **--template** option allows for generating an example script on the `stdout`.
### API Changes
- Two of the main class `obiseq.SeqWorker` and `obiseq.SeqWorker` have their declaration changed.
Both now return two values a `obiseq.BioSequenceSlice` and an `error`. This allow a worker to
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zero, which is equivalent to filter out the input sequence.
### Enhancement
- In `obitag` if the reference database contains sequences annotated by taxid not referenced in the taxonomy,
the corresponding sequences are discarded from the reference database and a warning indicating the sequence id
and the wrong taxid is emitted.
- The bug corrected in the parsing of EMBL and Genbank files as implemented in version 4.1.2 of OBITools4,
potentially induced some reduction in the performance of the parsing. This should have been now fixed.
- In the same idea, parsing of genbank and EMBL files were reading and storing in memory not only
the sequence
but also the annotations (features table). Up to now none of the obitools are using this information, but
but also the annotations (features table). Up to now none of the OBITools are using this information, but
with large complete genomes, it is occupying a lot of memory. To reduce this impact, the new version of
the parser doesn't any more store in memory the annotations by default.
- Add a **--taxonomic-path** to `obiannotate`. The option adds a `taxonomic_path` tag to sequences describing
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root of the taxonomy. The latest corresponds to the taxid of the sequence. If a sequence is not annotated by
a taxid, as usual the sequence is assumed having the taxid 1 (the root of the taxonomy).
### Bug fixes
- Fix a bug in the parsing of the JSON header of FASTA and FASTQ files occurring when a string includes a curly
brace.
## February 16th, 2024. Release 4.1.2
### Bug fixes