Commit 34a0ebcb authored by Mathieu Giraud's avatar Mathieu Giraud

doc/algo.org: update examples, using only test from demo/

parent cb7d8fa3
......@@ -754,17 +754,12 @@ This file will be relatively small (a few kB or MB) and can be taken again as an
** Advanced usage
#+BEGIN_SRC sh
./vidjil-algo -c clones -g germline/homo-sapiens.g:IGH -r 1 ./algo/tests/data/clones_simul.fa
./vidjil-algo -c clones -g germline/homo-sapiens.g -r 1 -n 5 -x 10000 demo/LIL-L4.fa
# Extracts the windows with at least 1 read each (-r 1, the default being -r 5)
# then cluster them into clones
#+END_SRC
#+BEGIN_SRC sh
./vidjil-algo -c clones -g germline/homo-sapiens.g:IGH -r 1 -n 5 ./algo/tests/data/clones_simul.fa
# Window extraction + clone clustering,
# with automatic clustering, distance five (-n 5)
# The result of the automatic clustering is in the .vidjil file
# and can been seen/edited in the web application.
# on the first 10,000 reads, then cluster them into clones
# with a second clustering step at distance five (-n 5)
# The result of this second is in the .vidjil file ('clusters')
# and can been seen and edited in the web application.
#+END_SRC
#+BEGIN_SRC sh
......
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