Commit dd92fbb3 authored by Mathieu Giraud's avatar Mathieu Giraud

Merge branch 'feature-a/release' into 'dev'

Release 2020.06

See merge request !727
parents 39982e0e 73450ab9
Pipeline #151436 passed with stages
in 14 minutes and 55 seconds
......@@ -16,6 +16,7 @@ build_doc:
# branch name should contain doc before the first /
# eg.: doc/blabla or feature-adoc/blabla
- /^feature-.*a.*\/release$/
allow_failure: true
tags:
- cidocker
......
This changelog concerns vijil-algo, the algorithmic part (C++) of the Vidjil platform.
2020-06-12 The Vidjil Team
* New report of 'start of V' and 'end of J' positions #2138, improving the productivity estimation #2142
This is based on a streamlined alignment for reverse sequences (core/segment.cpp) !706
* Faster and improved probability computations (core/proba.cpp) !679
This will bring further speed-ups in a future release
* Ctrl-C now gracefully stops execution with a warning W09 and some output #4286
* Streamlined handling of warnings #3360, also reported with -c designations #3811
* Better and more reproducible speed and memory benchmarks (benchmark-releases.py, #4275) #918, new profiling #918
* Adoption of 'detected' term, renamed output files to '.detected.vdj.fa' #3413
* Updated documentation
* New and updated tests
* Better release process through a merge request template !685
2020-05-02 The Vidjil Team
* Bug closed (crash in very rare cases #4272)
......
# vidjil-algo 2020.05
# vidjil-algo 2020.06
**Command-line manual**
*The Vidjil team (Mathieu, Mikaël, Aurélien, Florian, Marc, Tatiana and Rayan)*
......@@ -496,11 +496,12 @@ as provided by `make germline`.
The CDR3/JUNCTION detection won't work with custom non-gapped V/J repertoires.
CDR3 are reported as *productive* when they come from an in-frame recombination
and when the full sequence does not contain any in-frame stop codons.
and when the sequence does not contain any in-frame stop codons.
Note that some other software only consider stop codons in the CDR3,
and may thus under-estimate non-productivity. Vidjil-algo looks for in-frame stop codons
on all the available sequence (and may sometimes over-estimate non-productivity when
the sequence contains intronic regions).
and may thus under-estimate non-productivity.
When the sequence is long enough to start before the start of the V gene
or to end after the end of the J gene, vidjil-algo do not consider these intronic sequences
in the productivity estimation.
The advanced `--analysis-cost` option sets the parameters used in the comparisons between
the clone sequence and the V(D)J germline genes. The default values should work.
......
Markdown is supported
0%
or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment