Skip to content
GitLab
Menu
Projects
Groups
Snippets
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
vidjil
vidjil
Commits
d05b8ed1
Commit
d05b8ed1
authored
Mar 11, 2019
by
Mathieu Giraud
Browse files
tests: --grep-reads
See
#3785
.
parent
c06c7fc2
Changes
3
Hide whitespace changes
Inline
Side-by-side
algo/tests/should-get-tests/combo-grep-reads.should-get
0 → 100644
View file @
d05b8ed1
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -x 2000 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH --grep-reads GAGAGGTTACTATGATAGTAGTGGTTATTACGGGGTAGGGCAGTACTACT $VIDJIL_DATA/Stanford_S22.fasta ; cat out/seq/clone.fa-1
# See also label-grep-reads.should-get
$ Keep only one windows, the one given by -W, with only 2 reads in the first 2000 reads (it is actually the second clone in Stanford_S22.fasta)
1: keep 1 windows in 2 reads
$ Tbere are the three IGHV/D/J genes in out/seq/clone.fa-1
3:>IGH
$ There are 2 reads in out/seq/clone.fa-1
2:>lcl
algo/tests/should-get-tests/
stanford-labels-FaW
.should-get
→
algo/tests/should-get-tests/
labels-grep-reads
.should-get
View file @
d05b8ed1
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -x 2000 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH --out-reads --label-filter --label GAGAGGTTACTATGATAGTAGTGGTTATTACGGGGTAGGGCAGTACTACT $VIDJIL_DATA/Stanford_S22.fasta ; cat out/seq/clone.fa-1
# See also combo-grep-reads.should-get
$ Keep only one windows, the one given by -W, with only 2 reads in the first 2000 reads (it is actually the second clone in Stanford_S22.fasta)
1: keep 1 windows in 2 reads
...
...
algo/tests/should-get-tests/vidjil-help-advanced.should-get
View file @
d05b8ed1
...
...
@@ -17,4 +17,4 @@ $ Display advanced options
: custom Cost
$ Correct number of options
B5
1
:^ -
B5
2
:^ -
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment