Commit 3ab644ff authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil: release 2015.06

parent fef236dd
This changelog concerns the algorithmic part (C++) of Vidjil.
2015-06-XX The Vidjil Team
2015-06-05 The Vidjil Team
* New default trim option (-t 100), considering only the relevant ends of the germline genes
* Better segmentation heuristic when there are few k-mers (core/segment.cpp)
* Better TRA/TRD locus analysis (-i), including both Vd-(Dd)-Ja and Dd-Ja recombinations (core/germline.cpp)
* Better incomplete TRD and Dh/Jh analysis (-i), including up/downstream region of D genes (core/germline.cpp)
* Better computation of the reference length for the coverage information, considering all reads of each clone
* Better unexpected recombination analysis (-2), with information on the locus used (core/segment.cpp)
* Streamlined again unsegmentation causes (core/segment.cpp)
* Streamlined again unsegmentation causes and removed delta_{min,max} for the heuristic (core/segment.cpp)
* Refactored stats computation (core/read_storage.cpp)
* Updated build process
* Updated help (unsegmentation causes, clustering options)
* Bugs closed (segmentation with k-mers on the negative strand, clone output on stdout)
The next release will require a C++11 compiler. Static binaries will also be distributed.
* Updated help (unsegmentation causes, clustering options, -m option)
* Bugs closed (segmentation with k-mers on the negative strand, e-value computation, clone output on stdout)
* New and updated unit and functional tests, and faster functional tests
2015-05-08 The Vidjil Team
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