Changelog.md

Changelog

API only.

• 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 It has been replaced by two functions: UnitigMap::mappedSequenceToString() and UnitigMap::referenceUnitigToString().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.