Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
vidjil
Project overview
Project overview
Details
Activity
Releases
Repository
Repository
Files
Commits
Branches
Tags
Contributors
Graph
Compare
Issues
1,696
Issues
1,696
List
Boards
Labels
Service Desk
Milestones
Merge Requests
89
Merge Requests
89
CI / CD
CI / CD
Pipelines
Jobs
Schedules
Operations
Operations
Incidents
Environments
Packages & Registries
Packages & Registries
Container Registry
Analytics
Analytics
CI / CD
Repository
Value Stream
Snippets
Snippets
Members
Members
Collapse sidebar
Close sidebar
Activity
Graph
Create a new issue
Jobs
Commits
Issue Boards
Open sidebar
vidjil
vidjil
Commits
50238f19
Commit
50238f19
authored
Mar 07, 2019
by
Mikaël Salson
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
algo/: Separate the sequence name with a tab in all case
This should ease parsing the output.
parent
1f3d1d48
Changes
3
Hide whitespace changes
Inline
Side-by-side
Showing
3 changed files
with
16 additions
and
1 deletion
+16
-1
algo/core/segment.cpp
algo/core/segment.cpp
+1
-1
algo/tests/data/segment-or-not.fa
algo/tests/data/segment-or-not.fa
+11
-0
algo/tests/should-get-tests/tabs-in-output.should-get
algo/tests/should-get-tests/tabs-in-output.should-get
+4
-0
No files found.
algo/core/segment.cpp
View file @
50238f19
...
...
@@ -361,7 +361,7 @@ string Segmenter::getInfoLine() const
{
string
s
=
""
;
s
+=
(
segmented
?
""
:
"! "
)
+
info
;
s
+=
(
segmented
?
""
:
"
\t
! "
)
+
info
;
s
+=
" "
+
info_extra
;
s
+=
" "
+
segmented_germline
->
code
;
s
+=
" "
+
string
(
segmented_mesg
[
because
])
;
...
...
algo/tests/data/segment-or-not.fa
0 → 100644
View file @
50238f19
>lcl|FLN1FA002RWEZA.1|
ggctggagtgggtttcatacattagtagtaatagtggtgccatatactacgcagactctgtgaagggccgattcaccatc
tccagaaacaatgccaaggactcactgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgc
gagagcgatcccccggtattactatgatactagtggcccaaacgactactggggccagggaaccctggtcaccgtctcct
cag
>unsegmented
CGAATGCCTACATAGGGCTGGACGGCGTGCGTATTCCGTTACTACGACGATTCAAGGTAGTACAGCAAGACCACTGACCACTCCCGTGAGATATTTACCGAACGCCATTACGTATTGACACCGCAGTAATGACCTGGGTGGGGCATAGTCAAATTTCTGATGCTGGATAGTTTAATCCGCAGAGATTTTGTACTTGGCGATTGCTACACGATGTGTAGTAAATGATGAATATTCATAATCACCTTTCTGTGCCGATGGCATAGGGGGACCAATACCTCTGTTCGATGAACTAAGCTGGGA
>unexpected-IGHV-TRGJ
ATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAG
CGATCCCCCGGTATTACTATGATACTAGTGGCCCAAAC
atagtagtgattggatcaagacgtttgcaaaagggactaggctcatagtaacttcgcctg
\ No newline at end of file
algo/tests/should-get-tests/tabs-in-output.should-get
0 → 100644
View file @
50238f19
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -2 -c designations -g $VIDJIL_DIR/germline $VIDJIL_DATA/segment-or-not.fa
$ Check that output has one tab for each sequence
3:^>.*\t
\ No newline at end of file
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