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OBITools4
Release_4.1.1
Eric Coissac's avatar
Eric Coissac
@coissac
773ca2e8 · Update release date · 
Release 4.1.1

December 20th, 2023. Release 4.1.1

New feature

  • In obimatrix a --transpose option allows to transpose the produced matrix table in CSV format.
  • In obitpairing and obipcrtag two new options --exact-mode and --fast-absolute to control the heuristic used in the alignment procedure. --exact-mode allows for disconnecting the heuristic and run the exact algorithm at the cost of a speed. --fast-absolute change the scoring schema of the heuristic.
  • In obiannotate adds the possibility to annotate the first match of a pattern using the same algorithm than the one used in obipcr and obimultiplex. For that four option were added :
    • --pattern : to specify the pattern. It can use IUPAC codes and position with no error tolerated has to be followed by a # character.
    • --pattern-name : To specify the names of the slot used to report the results. Default is pattern
    • --pattern-error : To specify the maximum number of error tolerated during matching process.
    • --allows-indels : By default considered errors are mismatched, this flag allows for indels. Only the first match is reported if several occurrences exist. If no match is found on direct strand then pattern is looked for on the reverse complemented strand of the sequence.

Enhancement

  • For efficiency purposes, now the obiuniq command run on disk by default. Consequently, the --on-disk option has been replaced by --in-memory to ask explicitly to use memory.
  • Adds an option --penalty-scale to the obipairing and obipcrtag command to fine tune the pairing score in the system of the alignment procedure by applying a scaling factor to the mismatch score and the gap score relatively to the match score.

Bug fixes

  • In obicsv, the --keep count was not equivalent to --count.
  • In obipairing and obipcrtag, correct a bug in the alignment procedure leading to negative scores.
  • In obimultiplex, correct a bug leading to a miss-read of the ngsfilter file when tags where written in lower case.
  • In obitag, correct a bug leading to the annotation by taxid 1 (root) all the sequences having a 100% match with one the reference sequence.