ASGART v2.0

Changelog

• ASGART does not differentiate anymore between strand A and strand B,
  but simply works on an arbitrarily large set of files. Thus, the
  user SHOULD PROVIDE EACH FILE ONLY ONCE. Moreover, it is not
  necessarily to concatenate multiple input files in a single one
  anymore. This breaking change should give more flexibility to
  the users and potentially simplifies pipelines.
• The ASGART automaton has been rewritten from scratch to take into
  account interlaced SDs at nearly no cost in computation time. For
  this reason, interlaced duplication families research is now the
  only and default mode.
• ASGART will now remove large expanses of nucleotides to ignore (Ns
  and/or masked ones) in processed strands, thus slightly improving
  performances.
• Taking advantage of these new features, the parallelization system
  has been rewritten to (i) introduce parallelism at the scale of the
  automaton; and (ii) make use of the “natural” aforementioned
  breakpoints as delimiters for chunks to process in parallel. By
  doing so, it is guaranteed (i) that no duplication families that
  would be situated between two chunks will be missed; (ii) that
  ASGART will make use of available cores even when processing less
  chunks than authorized threads.
• ASGART will now make use of the trimming feature to reduce memory
  consumption. The suffix array will be built only for the trimmed
  part, instead than for the whole input. The whole input will then be
  compared to the trimmed part, contrary to what happened in version
  1.x. Such an arrangement sacrifice some CPU power in exchange of a
  strongly reduced memory consumption when processing trimmed inputs.
  It can be used to process large sequences by trimming them in
  several consecutive subsequences, then mergin the results later on.
• The JSON and GFF3 output formats have been modified to reflect the
  duplication families clustering. Please note that they are thus
  incompatible with previous versions JSON files.
• A new tool asgart-concat has been added to safely concatenate JSON
  files resulting from partial runs on the same dataset. Its intended
  use is to easily merge the results from multiple runs on the same
  dataset with different settings, e.g. direct & palindromic
  duplications or if the workload was divided in multiple sub-jobs
  using trimming.
• Plotting utilities have been modified to reflect these changes.
• The automaton will progressively grow the maximal gap size when
  extending large duplications, thus letting larger duplications arms
  be found in a less fragmented way.
• The logging system has been improved to be more detailed and more
  coherent in its way to present informations.
• Minor technical issues have been resolved: ASGART will correctly
  only use the ID field of FASTA files and not the subsequent
  informations; the progress bar does not glitch anymore.