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Release-notes.md
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Release-notes.md
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# OBITools release notes
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## Latest changes
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## March 2nd, 2025. Release 4.3.0
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A new documentation website is available at https://obitools4.metabarcoding.org.
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Its development is still in progress.
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### Breaking changes
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- In `obimultiplex`, the short version of the **--tag-list** option used to specify the list
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of tags and primers to be used for the demultiplexing has been changed from `-t` to `-s`.
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- In `obimultiplex`, the short version of the **--tag-list** option used to
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specify the list of tags and primers to be used for the demultiplexing has
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been changed from `-t` to `-s`.
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- The command `obifind` is now renamed `obitaxonomy`.
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- The **--taxdump** option used to specify the path to the taxdump containing the NCBI taxonomy
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has been renamed to **--taxonomy**.
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- The **--taxdump** option used to specify the path to the taxdump containing
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the NCBI taxonomy has been renamed to **--taxonomy**.
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### Bug fixes
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- Correction of a bug when using paired sequence file with the **--out** option.
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- Correction of a bug in `obitag` when trying to annotate very short sequence of
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4 bases or less.
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- In `obipairing`, correct the stats `seq_a_single` and `seq_b_single` when
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on right alignment mode
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@ -21,16 +31,32 @@
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the batch size and not reading the qualities from the fastq files as `obiuniq`
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is producing only fasta output without qualities.
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- In `obitag`, correct the wrong assignment of the **obitag_bestmatch**
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attribute.
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- In `obiclean`, the **--no-progress-bar** option disables all progress bars,
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not just the data.
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- Several fixes in reading FASTA and FASTQ files, including some code
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simplification and factorization.
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- Fixed a bug in all obitools that caused the same file to be processed
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multiple times, when specifying a directory name as input.
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### New features
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- `obigrep` add a new **--valid-taxid** option to keep only sequence with a
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valid taxid
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- `obiclean` add a new **--min-sample-count** option with a default value of 1,
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asking to filter out sequences which are not occurring in at least the
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specified number of samples.
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- `obitoaxonomy` a new **--dump|D** option allows for dumping a sub-taxonomy.
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- Taxonomy dump can now be provided as a four-columns CSV file to the **--taxonomy**
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option.
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- Taxonomy dump can now be provided as a four-columns CSV file to the
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**--taxonomy** option.
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- NCBI Taxonomy dump does not need to be uncompressed and unarchived anymore. The
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path of the tar and gziped dump file can be directly specified using the
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allow the processing of the rare fasta and fastq files not recognized.
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- In `obiscript`, adds new methods to the Lua sequence object:
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- `md5_string()`: returning the MD5 check sum as a hexadecimal string,
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- `subsequence(from,to)`: allows extracting a subsequence on a 0 based
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coordinate system, upper bound excluded like in go.
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- `reverse_complement`: returning a sequence object corresponding to the reverse complement
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of the current sequence.
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- `md5_string()`: returning the MD5 check sum as a hexadecimal string,
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- `subsequence(from,to)`: allows extracting a subsequence on a 0 based
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coordinate system, upper bound excluded like in go.
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- `reverse_complement`: returning a sequence object corresponding to the
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reverse complement of the current sequence.
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### Enhancement
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- In every *OBITools* command, the progress bar is automatically deactivated
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when the standard error output is redirected.
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- Because Genbank and ENA:EMBL contain very large sequences, while OBITools4
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are optimized As Genbank and ENA:EMBL contain very large sequences, while
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OBITools4 is optimized for short sequences, `obipcr` faces some problems
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with excessive consumption of computer resources, especially memory. Several
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improvements in the tuning of the default `obipcr` parameters and some new
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features, currently only available for FASTA and FASTQ file readers, have
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been implemented to limit the memory impact of `obipcr` without changing the
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computational efficiency too much.
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- Logging system and therefore format, have been homogenized.
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### Change of git repository
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@ -54,35 +95,16 @@
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Take care for using the new install script for retrieving the new version.
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```bash
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curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh \
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curl -L https://metabarcoding.org/obitools4/install.sh \
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| bash
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```
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or with options:
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```bash
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curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh \
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curl -L https://metabarcoding.org/obitools4/install.sh \
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| bash -s -- --install-dir test_install --obitools-prefix k
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```
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### CPU limitation
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- By default, *OBITools4* tries to use all the computing power available on
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your computer. In some circumstances this can be problematic (e.g. if you
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are running on a computer cluster managed by your university). You can limit
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the number of CPU cores used by *OBITools4* or by using the **--max-cpu**
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option or by setting the **OBIMAXCPU** environment variable. Some strange
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behavior of *OBITools4* has been observed when users try to limit the
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maximum number of usable CPU cores to one. This seems to be caused by the Go
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language, and it is not obvious to get *OBITools4* to run correctly on a
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single core in all circumstances. Therefore, if you ask to use a single
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core, **OBITools4** will print a warning message and actually set this
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parameter to two cores. If you really want a single core, you can use the
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**--force-one-core** option. But be aware that this can lead to incorrect
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calculations.
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### New features
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- The output of the obitools will evolve to produce results only in standard
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formats such as fasta and fastq. For non-sequential data, the output will be
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in CSV format, with the separator `,`, the decimal separator `.`, and a
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@ -161,31 +183,23 @@
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The CSV format used allows for comment lines starting with `#` character.
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Special data lines starting with `@param` in the first column allow configuring the algorithm. The options **--template** provided an over
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commented example of the CSV format, including all the possible options.
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### CPU limitation
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### Enhancement
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- By default, *OBITools4* tries to use all the computing power available on
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your computer. In some circumstances this can be problematic (e.g. if you
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are running on a computer cluster managed by your university). You can limit
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the number of CPU cores used by *OBITools4* or by using the **--max-cpu**
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option or by setting the **OBIMAXCPU** environment variable. Some strange
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behavior of *OBITools4* has been observed when users try to limit the
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maximum number of usable CPU cores to one. This seems to be caused by the Go
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language, and it is not obvious to get *OBITools4* to run correctly on a
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single core in all circumstances. Therefore, if you ask to use a single
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core, **OBITools4** will print a warning message and actually set this
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parameter to two cores. If you really want a single core, you can use the
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**--force-one-core** option. But be aware that this can lead to incorrect
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calculations.
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- In every *OBITools* command, the progress bar is automatically deactivated
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when the standard error output is redirected.
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- Because Genbank and ENA:EMBL contain very large sequences, while OBITools4
|
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are optimized As Genbank and ENA:EMBL contain very large sequences, while
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OBITools4 is optimized for short sequences, `obipcr` faces some problems
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with excessive consumption of computer resources, especially memory. Several
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improvements in the tuning of the default `obipcr` parameters and some new
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features, currently only available for FASTA and FASTQ file readers, have
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been implemented to limit the memory impact of `obipcr` without changing the
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computational efficiency too much.
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- Logging system and therefore format, have been homogenized.
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### Bug
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- In `obitag`, correct the wrong assignment of the **obitag_bestmatch**
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attribute.
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- In `obiclean`, the **--no-progress-bar** option disables all progress bars,
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not just the data.
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- Several fixes in reading FASTA and FASTQ files, including some code
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simplification and factorization.
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- Fixed a bug in all obitools that caused the same file to be processed
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multiple times, when specifying a directory name as input.
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## April 2nd, 2024. Release 4.2.0
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