Commit b878a714 authored by Mikaël Salson's avatar Mikaël Salson

Merge branch 'feature-a/3811-warnings-c-designations' into 'dev'

Report clone warnings with -c designations

Closes #3811

See merge request !708
parents 0bffa98c ff306030
Pipeline #150556 failed with stages
in 6 minutes and 26 seconds
......@@ -6,7 +6,7 @@ $ Segments the read on TRB (the information is given twice, stdout + .vidjil)
$ The FineSegmenter outputs a segmentation without any D
1: clone-001--TRB--.*--TRBV7-2--TRBJ2-3
$ There is a segmentation in the .vidjil, but without any D
$ The recombination is properly designated, without any D
1:"name": "TRBJ2-3.01"
0:"name": "TRBD
1:"name": "TRBV7-2.01"
......@@ -15,3 +15,15 @@ $ There is a warning on multiple candidate assignations
1:"code": "W69"
1:equal probability: TRBV7-2.0[12] TRBV7-2.0[12]"
!LAUNCH: $VIDJIL_DIR/$EXEC -c designations -g $VIDJIL_DIR/germline/homo-sapiens.g:TRB $VIDJIL_DATA/trb-only-VJ.fa
!OUTPUT_FILE: out/trb-only-VJ.vidjil
$ With -c designation, the recombination is properly designated, without any D
1:"name": "TRBJ2-3.01"
0:"name": "TRBD
1:"name": "TRBV7-2.01"
$ With -c designation, there is a warning on multiple candidate assignations
1:"code": "W69"
1:equal probability: TRBV7-2.0[12] TRBV7-2.0[12]"
......@@ -1725,6 +1725,7 @@ int main (int argc, char **argv)
}
s.toOutput(clone);
s.checkWarnings(clone);
clone->set("germline", g->code);
nb_segmented_by_germline[g->code]++ ;
......
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