Commit d90203ba authored by Mathieu Giraud's avatar Mathieu Giraud

tests: update, bikeshed strings

parent 1d792438
......@@ -13,7 +13,7 @@
0:Extracting windows
# '-c designations', one time
1:Segmenting V.D.J
1:Designating V.D.J
# '-c germlines'
1:Discovering germlines
......
......@@ -8,17 +8,17 @@ cd $VIDJIL_DIR ; sh help-examples.sh
# Run 7 times (-h + 6 examples)
7:vidjil-algo -- V.D.J recombinations analysis
# '-c clone', three times
# '-c clones', three times
3: end of clones
# '--filter-reads'
1:Detecting
1:Detecting V.D.J recombinations$
# '-c windows'
1:Extracting windows
# '-c clones' / '-c windows'
4:Detecting V.D.J recombinations and
# '-c designations'
1:Segmenting V.D.J
1:Designating V.D.J recombinations
# '-c germlines'
1:Discovering germlines
......
......@@ -3,7 +3,7 @@
# Testing '-w all' option
$ The junctions are the reads
1: considering all analyzed reads as windows
1: considering all detected reads as windows
1: found 13141 windows in 13153 reads
$ Only the first 12 clones have 2 reads
......
!LAUNCH: $VIDJIL_DIR/$EXEC --all -w all -g $VIDJIL_DIR/germline/homo-sapiens.g $VIDJIL_DATA/s-somatic.fa ; cat out/s-somatic.vidjil | python $VIDJIL_DIR/tools/format_json.py -1
$ No clustering due to -w all
1: considering all analyzed reads as windows
1: considering all detected reads as windows
$ Warning on similar clones in json ('warn' because this is a clone in the first 10 clones)
1: "code": "W53", "level": "warn", "msg": "Similar to clone #1 .* IGHV3-48.01 .* IGHJ4.02"
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