obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-06-29 16:20:46 +00:00
Code Issues Packages Projects Releases Wiki Activity

update the release notes for version 4.4.0

Browse Source
This commit is contained in:
Eric Coissac
2025-03-01 12:56:39 +01:00
parent 5f9182d25b
commit 996ec69bd9
1 changed files with 24 additions and 1 deletions
Download Patch File Download Diff File Expand all files Collapse all files

25
Release-notes.md
View File

@ -1,10 +1,15 @@
# OBITools release notes # OBITools release notes
## March 2nd, 2025. Release 4.3.0 ## March 1st, 2025. Release 4.4.0
A new documentation website is available at https://obitools4.metabarcoding.org. A new documentation website is available at https://obitools4.metabarcoding.org.
Its development is still in progress. Its development is still in progress.
The biggest step forward in this new version is taxonomy management.
The new version is now able to handle taxonomic identifiers that are not just integer values. This is a first step towards an easy way to handle other taxonomy databases soon, such as the GBIF or Catalogue of Life taxonomies.
This version is able to handle files containing taxonomic information created by previous versions of OBITools, but files created by this new version may have some problems to be analysed by previous versions, at least for the taxonomic information.
### Breaking changes ### Breaking changes
- In `obimultiplex`, the short version of the **--tag-list** option used to - In `obimultiplex`, the short version of the **--tag-list** option used to
@ -75,8 +80,24 @@ Its development is still in progress.
### Enhancement ### Enhancement
- All obitools now have a **--taxonomy** option. If specified, the taxonomy is
loaded first and taxids annotating the sequences are validated against that
taxonomy. A warning is issued for any invalid taxid and for any taxid that
is transferred to a new taxid. The **--update-taxid** option allows these
old taxids to be replaced with their new equivalent in the result of the
obitools command.
- The scoring system used by the `obipairing` command has been changed to be
more coherent. In the new version, the scores associated to a match and a
mismatch involving a nucleotide with a quality score of 0 are equal. Which
is normal as a zero quality score means a perfect indecision on the read
nucleotide, therefore there is no reason to penalize a match differently
from a mismatch (see
https://obitools4.metabarcoding.org/docs/commands/alignments/obipairing/exact-alignment/).
- In every *OBITools* command, the progress bar is automatically deactivated - In every *OBITools* command, the progress bar is automatically deactivated
when the standard error output is redirected. when the standard error output is redirected.
- Because Genbank and ENA:EMBL contain very large sequences, while OBITools4 - Because Genbank and ENA:EMBL contain very large sequences, while OBITools4
are optimized As Genbank and ENA:EMBL contain very large sequences, while are optimized As Genbank and ENA:EMBL contain very large sequences, while
OBITools4 is optimized for short sequences, `obipcr` faces some problems OBITools4 is optimized for short sequences, `obipcr` faces some problems
@ -85,8 +106,10 @@ Its development is still in progress.
features, currently only available for FASTA and FASTQ file readers, have features, currently only available for FASTA and FASTQ file readers, have
been implemented to limit the memory impact of `obipcr` without changing the been implemented to limit the memory impact of `obipcr` without changing the
computational efficiency too much. computational efficiency too much.
- Logging system and therefore format, have been homogenized. - Logging system and therefore format, have been homogenized.
## August 2nd, 2024. Release 4.3.0
### Change of git repository ### Change of git repository