Release 4.0.4

August 27th, 2023. Release 4.0.4


  • Patch a bug in the install-script for correctly follow download redirection.
  • Patch a bug in obitagpcr to consider the renaming of the forward_mismatch and reverse_mismatch tags to forward_error and reverse_error.


  • Comparison algorithms in obitag and obirefidx take more advantage of the data structure to limit the number of alignments actually computed. This increase a bit the speed of both the software. obirefidx is nevertheless still too slow compared to my expectation.
  • Switch to a parallel version of the gzip library, allowing for high speed compress and decompress operation on files.

New feature

  • In every OBITools, writing an empty sequence (sequence of length equal to zero) through an error and stops the execution of the tool, except if the --skip-empty option is set. In that case, the empty sequence is ignored and not printed to the output. When output involved paired sequence the --skip-empty option is ignored.
  • In obiannotate adds the --set-identifier option to edit the sequence identifier
  • In obitag adds the --save-db option allowing at the end of the run of obitag to save a modified version of the reference database containing the computed index. This allows next time using this partially indexed reference library to accelerate the taxonomic annotations.
  • Adding of the function gsub to the expression language for substituting string pattern.