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76 lines
3.7 KiB
Markdown
76 lines
3.7 KiB
Markdown
# OBITools release notes
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## On going changes
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## March 7th, 2023. Release 4.0.1
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### Corrected bugs
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- Makes progress bar updating at most 10 times per second.
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- Makes the command exiting on error if undefined options are used.
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### Enhancement
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- *OBITools* are automatically processing all the sequences files contained in a directory and its sub-directory
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recursively if its name is provided as input. To process easily Genbank files, the corresponding filename
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extensions have been added. Today the following extensions are recognized as sequence files : `.fasta`, `.fastq`,
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`.seq`, `.gb`, `.dat`, and `.ecopcr`. The corresponding gziped version are also recognized (e.g. `.fasta.gz`)
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### New features
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- Takes into account the `OBIMAXCPU` environmental variable to limit the number of CPU cores used
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by OBITools in bash the below command will limit to 4 cores the usage of OBITools
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```bash
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export OBICPUMAX=4
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```
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- Adds a new option --out|-o allowing to specify the name of an outpout file.
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```bash
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obiconvert -o xyz.fasta xxx.fastq
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```
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is thus equivalent to
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```bash
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obiconvert xxx.fastq > xyz.fasta
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````
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That option is actually mainly useful for dealing with paired reads sequence files.
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- Some OBITools (now `obigrep` and `obiconvert`) are capable of using paired read files.
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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.
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- Adding of the function `ifelse` to the expression language for computing conditionnal values.
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- Adding two function to the expression language related to sequence conposition : `composition` and `gcskew`.
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Both are taking a sequence as single argument.
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## February 18th, 2023. Release 4.0.0
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It is the first version of the *OBITools* version 4. I decided to tag then following two weeks
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of intensive data analysis with them allowing to discover many small bugs present in the previous
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non-official version. Obviously other bugs are certainly persent in the code, and you are welcome
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to use the git ticket system to mention them. But they seems to produce now reliable results.
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### Corrected bugs
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- On some computers the end of the output file was lost, leading to the loose of sequences and
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to the production of incorrect file because of the last sequence record, sometime truncated in
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its middle. This was only occurring when more than a single CPU was used. It was affecting every obitools.
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- The `obiparing` software had a bug in the right aligment procedure. This led to the non alignment
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of very sort barcode during the paring of the forward and reverse reads.
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- The `obipairing` tools had a non deterministic comportment when aligning a paor very low quality reads.
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This induced that the result of the same low quality read pair was not the same from run to run.
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### New features
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- Adding of a `--compress|-Z` option to every obitools allowing to produce `gz` compressed output. OBITools
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were already able to deal with gziped input files transparently. They can now produce their résults in the same format.
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- Adding of a `--append|-A` option to the `obidistribute` tool. It allows to append the result of an
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`obidistribute` execution to preexisting files.
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- Adding of a `--directory|-d` option to the `obidistribute` tool. It allows to declare a secondary
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classification key over the one defined by the '--category|-c` option. This extra key leads to produce
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directories in which files produced according to the primary criterion are stored.
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- Adding of the functions `subspc`, `printf`, `int`, `numeric`, and `bool` to the expression language.
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