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OBITools4
Release_4.0.2
Eric Coissac's avatar
Eric Coissac
@coissac
e516cce0 · Release 4.0.2 · 
Release 4.0.2

March 31th, 2023. Release 4.0.2

Compiler change

OBItools4 requires now GO 1.20 to compile.

New features

  • Add the possibility for looking pattern with indels. This has been added to obimultiplex through the --with-indels option.
  • Every obitools command has a --pprof option making the command publishing a profiling web site available at the address : http://localhost:8080/debug/pprof/
  • A new obiconsensus command has been added. It is a prototype. It aims to build a consensus sequence from a set of reads. The consensus is estimated for all the sequences contained in the input file. If several input files, or a directory name are provided the result contains a consensus per file. The id of the sequence is the name of the input file depleted of its directory name and of all its extensions.
  • In obipcr an experimental option --fragmented allows for spliting very long query sequences into shorter fragments with an overlap between the two contiguous fragment insuring that no amplicons are missed despite the split. As a site effect some amplicon can be identified twice.
  • In obipcr the -L option is now mandatory.

Enhancement

  • Add support for IUPAC DNA code into the DNA sequence LCS computation and an end free gap mode. This impact obitag and obimultiplex in the --with-indels mode.
  • Print the synopsis of the command when an error is done by the user at typing the command
  • Reduced the memory copy and allocation during the sequence creation.

Corrected bugs

  • Better management of non-existing files. The produced error message is not yet perfectly clear.
  • Patch a bug leading with some programs to crash because of : "empty batch pushed on the channel"
  • Patch a bug when directory names are used as input data name preventing the system to actually analyze the collected files.
  • Make the --help or -h options working when mandatory options are declared
  • In obimultiplex correct a bug leading to a wrong report of the count of reverse mismatch for sequences in reverse direction.
  • In obimultiplex correct a bug when not enough space exist between the extremities of the sequence and the primer matches to fit the sample identification tag
  • In obipcr correction of bug leading to miss some amplicons when several amplicons are present on the same large sequence.