Commit 17a4c443 authored by Vidjil's avatar Vidjil Committed by Mathieu Giraud

vidjil-algo: prepare CHANGELOG for release 2018.07

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This changelog concerns vijil-algo, the algorithmic part (C++) of the Vidjil platform.
2018-07-xx The Vidjil Team
* New default option -Z 3, speeding up the full analysis of clones with a pre-processing based on k-mers #3298
Processes with `-c segment` or with large `-z` values will be between 2x and 15x faster (vidjil.cpp, core/filter.cpp)
* Integrated and extended up/downstream regions, improving analysis of heavily deleted 3' genes (germline/) #3008 #3009
* Corrected the heuristic in borderline cases with overlapping VJ affectations (core/affectanalyser.cpp) #3296
* Streamlined handling of seeds, enabling the use of aliases with -s (core/tools.cpp) #3293
* Refactored option processing for vidjil-algo with CLI11 (lib/CLI11.hpp, vidjil.cpp) #2732
* Improved build time up to 40% (lib/json_fwd.h) #3307
* Updated third-party library (lib/json.hpp) #2935
* Improved build and release process, supporting also g++ 7.3 and testing several compilers (.gitlab-ci.yml) #3002 #3015
* Removed unused code and CI parts #3294 #3287
* Refactored and re-enabled code coverage, making it publicly accessible on Gitlab (algo/Makefile, .gitlab-ci.yml) #1696
* New and updated unit and functional tests
2018-06-14 The Vidjil Team
* New experimental option -Z to speed-up the full analysis with a pre-processing based on k-mers (core/filter.cpp) #920
* New experimental analysis of Ikaros/ERG recombinations (germline/homo-sapiens-ikaros.g) #2139
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