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vidjil
vidjil
Commits
d90203ba
Commit
d90203ba
authored
Feb 11, 2021
by
Mathieu Giraud
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tests: update, bikeshed strings
parent
1d792438
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algo/tests/should-get-tests/help-doc-examples.should
algo/tests/should-get-tests/help-doc-examples.should
+1
-1
algo/tests/should-get-tests/help-examples.should
algo/tests/should-get-tests/help-examples.should
+5
-5
algo/tests/should-get-tests/w-all.should
algo/tests/should-get-tests/w-all.should
+1
-1
algo/tests/should-get-tests/warning-similar.should
algo/tests/should-get-tests/warning-similar.should
+1
-1
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algo/tests/should-get-tests/help-doc-examples.should
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d90203ba
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@@ -13,7 +13,7 @@
0:Extracting windows
# '-c designations', one time
1:
Segmen
ting V.D.J
1:
Designa
ting V.D.J
# '-c germlines'
1:Discovering germlines
...
...
algo/tests/should-get-tests/help-examples.should
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d90203ba
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@@ -8,17 +8,17 @@ cd $VIDJIL_DIR ; sh help-examples.sh
# Run 7 times (-h + 6 examples)
7:vidjil-algo -- V.D.J recombinations analysis
# '-c clone', three times
# '-c clone
s
', three times
3: end of clones
# '--filter-reads'
1:Detecting
1:Detecting
V.D.J recombinations$
# '-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
...
...
algo/tests/should-get-tests/w-all.should
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d90203ba
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@@ -3,7 +3,7 @@
# Testing '-w all' option
$ The junctions are the reads
1: considering all
analyz
ed reads as windows
1: considering all
detect
ed reads as windows
1: found 13141 windows in 13153 reads
$ Only the first 12 clones have 2 reads
...
...
algo/tests/should-get-tests/warning-similar.should
View file @
d90203ba
!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
analyz
ed reads as windows
1: considering all
detect
ed 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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