v1.4.0

• Integration of Leon compressor into GATB-Core :

  • It means that the Leon file format can now be handled natively by all softwares relying upon GATB-Core. In other words, you can apply data processing on reads without decompression of the Leon file.
  • more details at https://github.com/GATB/gatb-core/wiki/Using-GATB-Core-integrated-Leon-compressor
  • unit tests + large-scale test suite of Leon compressor; cf. https://ci.inria.fr/gatb-core/view/Leon/job/tool-leon-functional-tests/lastBuild/console

• Time and memory optimisations :

  • Faster k-mer counting (inspired by KMC3 but not yet as fast :)

  • More efficient graph representation using compressed vectors (in GraphUnitigs.cpp)

  • Faster unitigs compaction (engineering improvements in BCALM code)

  • New compact encoding scheme to load the abundance values in memory (encoded on 8 bits, value range = 0 to 50k with 5% max error)

• Parameterizable graph simplifications steps (see Graph.hpp and Minia): optional tip-clipping, bulge and erroneous connection removal

• Preliminary support for loading unitigs (in GraphUnitigs.cpp) from a GFA1 graph format generated by BCALM (using scripts/convertToGFA.py in BCALM repository)

• Adding new ways to compile, making compilation easier :

  • Added a simple makefile to compile a GATB tool without CMake (see examples/Makefile)

  • Added support for Docker. Using docker/Dockerfile one can build a docker image containing GATB-core.

  • 2 new ways to compile example codes snippets :

    • cmake -DGATB_CORE_INCLUDE_EXAMPLES=True ..
      or
    • cd example ; make [folder]/[examplename.cpp] for instance, make kmer/kmer2 will compile kmer2.cpp

• Various bugfixes