Progress on the development

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2023-03-07 11:13:25 +07:00
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- Makes progress bar updating at most 10 times per second.
- Makes the command exiting on error if undefined options are used.
### Enhancement
- *OBITools* are automatically processing all the sequences files contained in a directory and its sub-directory
recursively if its name is provided as input. To process easily Genbank files, the corresponding filename
extensions have been added. Today the following extensions are recognized as sequence files : `.fasta`, `.fastq`,
`.seq`, `.gb`, `.dat`, and `.ecopcr`. The corresponding gziped version are also recognized (e.g. `.fasta.gz`)
### New features
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- Some OBITools (now `obigrep` and `obiconvert`) are capable of using paired read files.
Options have been added for this (**--paired-with** _FILENAME_, and **--paired-mode** _forward|reverse|and|andnot|xor_). This, in combination with the **--out** option shown above, ensures that the two matched files remain consistent when processed.
- Adding of the function `ifelse` to the expression language for computing conditionnal values.
- Adding two function to the expression language related to sequence conposition : `composition` and `gcskew`.
Both are taking a sequence as single argument.
## February 18th, 2023. Release 4.0.0
It is the first version of the *OBITools* version 4. I decided to tag then following two weeks