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Commit 9aa54572 authored by Mathieu Giraud's avatar Mathieu Giraud

repseq_vdj.py: VIDJIL_FINE with -2

We would like to test some unexpected recombinations.
Closes #3518.
parent 474af333
......@@ -249,7 +249,8 @@ def header_igblast_results(ff_fasta, ff_igblast):
### Vidjil
VIDJIL_FINE = '{directory}/vidjil-algo --header-sep "#" -c segment -3 -d -g {directory}/germline/homo-sapiens.g %s >> %s'
VIDJIL_FINE = '{directory}/vidjil-algo --header-sep "#" -c segment -2 -3 -d -g {directory}/germline/homo-sapiens.g %s >> %s'
VIDJIL_KMER = '{directory}/vidjil-algo -w 20 --header-sep "#" -b out -c windows -uuuU -2 -g {directory}/germline/homo-sapiens.g %s > /dev/null ; cat out/out.segmented.vdj.fa out/out.unsegmented.vdj.fa >> %s'
def should_results_from_vidjil_output(f_log):
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