Commit 83a6dd62 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil: prepare CHANGELOG for release 2018.01

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This changelog concerns the algorithmic part (C++) of Vidjil.
This changelog concerns vijil-algo, the algorithmic part (C++) of the Vidjil platform.
2018-01-xx The Vidjil Team
* Renamed program to 'vidjil-algo'
* Improved analysis of large deletions in V or J genes (core/segment.cpp) #2767
* Improved analysis of reads where V/J junction is close to an end, slightly shifting or shortening
the window (core/segment.cpp, core/windowExtractor.cpp) #2913
* Removed default homopolymer cost, improving detection on the majority of sequencers (core/dynprog.h) #2851
* Added warnings in the json output on some clones #2916
* Bug closed (clean some germinal sequences #2598)
* Cleaned folders, with demo data in demo/ and test data in algo/tests/data/ #2635 #2611
* Changed option processing library, trying CLI11 instead of docopt (lib/CLI11.hpp, tools/align.cpp) #926
* Streamlined packaging and Makefile, based on git #2255 #2630
* Updated build process (supporting g++ 4.8 to 7.2, clang from 3.3), warns on non-supported compilers #2614 #2615 #2631
* Updated help and online help, in particular on -f option #2076
* Refactored unit tests with TEST_TAP_EQUAL #2989
* New and updated unit and functional tests, including tests from documentation #1284 #2634
2017-09-08 The Vidjil Team
* New BAM input parser, refactored input parsers (core/bioreader.cpp, core/bam.cpp) #2016
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