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Changelog.md

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Changelog

API only.

  • 17-11-2023
    • Class ColoredCDBG exposes the function readGraph() which enables to load/read the graph in a colored de Bruijn graph without associating any colors to the unitigs. This enables to later color the graph with any input sequences.
  • 10-09-2023

    • Function CompactedDBG()::search() takes additional arguments:

      • get_nb_found_km: boolean indicating whether to report in the output the number of found k-mers per query
      • get_ratio_found_km: boolean indicating wether to report in the output the ratio of found k-mers per query

      Note that using either options de facto disable argument ratio_kmers and will impact running time as all k-mers of the queries will be searched for (ratio_kmers allows to stop the search early by detecting when the ratio_kmers threshold cannot be met).

  • 15-06-2022

    • Function CompactedDBG()::write() takes additional arguments with default values:

      • compress_output indicates whether the output should be compressed
      • write_index_file indicates whether an index file should be generated to enable faster graph loading
      • GFA_output, FASTA_output and BFG_output to select the output file format (previously, setting outputGFA set to false would automatically make write() output the graph in FASTA format).

      Beware that the new arguments come with default values which could override the default values of the previous versions of write(), e.g, the default value of parameter FASTA_output (write() with 8 parameters) could be used as the default value of parameter verbose if your code is not updated (write() with 5 parameters).

    • There exists two versions of CompactedDBG::read() and ColoredCDBG::read(), the "usual" (slower) graph reading function and the same function with an additional index graph file as input. Using the index graph file as input considerably speeds-up the graph loading in memory. The "usual" graph reading function will automatically use the graph index file if available.

  • 04-28-2022
    • Color files generated prior to version 1.0.6.2 are not compatible with version 1.0.6.2 and onward.
    • CompactedDBG::simplify() and ColoredCDBG::simplify() now return true even if no simplification was performed ("null-simplification" in case all input parameters are set to false). The goal is to only return false if the graph is invalid or in case of unexpected behavior.
  • 08-29-2018
    • UnitigColors::const_iterator only considers now the k-mer positions of the unitig mapping provided in the UnitigMap/UnitigColorMap parameter of UnitigColors::begin().
  • 08-28-2018
    • Functions CDBG_Data_t::serialize() and CCDBG_Data_t::serialize() have now one parameter which is a const_UnitigMap/const_UnitigColorMap reference representing the (reference) unitig to which the data are associated to.
  • 08-23-2018
    • Function UnitigMap::toString() was ambiguous as if it would generate the string of the mapped sequence or the string of the reference unitig used in the mapping. It has been replaced by two functions: UnitigMap::mappedSequenceToString() and UnitigMap::referenceUnitigToString().
  • 08-07-2018
    • Add de Bruijn graphs merging functions (CompactedDBG::merge() and ColoredCDBG::merge()) and addition assignment operators (CompactedDBG::operator+=() and ColoredCDBG::operator+=(), same as merge() but uses only one thread).
    • Add de Bruijn graphs comparison functions CompactedDBG::operator==(), CompactedDBG::operator!=(), ColoredCDBG::operator==() and ColoredCDBG::operator!=().
    • Delete CompactedDBG::empty() and ColoredCDBG::empty() to be consistent with STD containers (those functions were emptying the graph of its content while empty() of STD containers returns whether the container is empty). Now, to empty the graph, use CompactedDBG::clear() and ColoredCDBG::clear().
    • Major changes in the abstract class CDBG_Data_t and CCDBG_Data_t:
      • All the functions are now non-static.
      • Function join() is renamed concat() and works a bit differently (have a look at the doc). Quickly, join() was concatenating two unitigs A and B such that the result was A=AB and B was deleted from the graph. Now, concat() deletes A and B from the graph and adds a new unitig C=AB.
      • Function sub() is renamed extract().
      • Add the functions merge() and clear() which must be overloaded too in the derived class of CDBG_Data_t and CCDBG_Data_t.