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
1,701
Issues
1,701
List
Boards
Labels
Service Desk
Milestones
Merge Requests
92
Merge Requests
92
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
e2bff0aa
Commit
e2bff0aa
authored
Feb 29, 2016
by
Mathieu Giraud
1
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
core/segment.{h,cpp}: remember in AligBox the 'marked_pos' coming from the DP backtrack
parent
6e1d108c
Changes
2
Hide whitespace changes
Inline
Side-by-side
Showing
2 changed files
with
9 additions
and
1 deletion
+9
-1
algo/core/segment.cpp
algo/core/segment.cpp
+6
-1
algo/core/segment.h
algo/core/segment.h
+3
-0
No files found.
algo/core/segment.cpp
View file @
e2bff0aa
...
...
@@ -722,7 +722,8 @@ void align_against_collection(string &read, Fasta &rep, int forbidden_rep_id,
DynProg
dp
=
DynProg
(
sequence_or_rc
,
rep
.
sequence
(
r
),
dpMode
,
// DynProg::SemiGlobalTrans,
segment_cost
,
// DNA
reverse_both
,
reverse_both
);
reverse_both
,
reverse_both
,
rep
.
read
(
r
).
marked_pos
);
bool
onlyBottomTriangle
=
!
local
;
int
score
=
dp
.
compute
(
onlyBottomTriangle
,
BOTTOM_TRIANGLE_SHIFT
);
...
...
@@ -740,6 +741,10 @@ void align_against_collection(string &read, Fasta &rep, int forbidden_rep_id,
best_first_j
=
dp
.
first_j
;
box
->
ref_nb
=
r
;
box
->
ref_label
=
rep
.
label
(
r
)
;
if
(
!
local
)
dp
.
backtrack
();
box
->
marked_pos
=
dp
.
marked_pos_i
;
}
score_r
.
push_back
(
make_pair
(
score
,
r
));
...
...
algo/core/segment.h
View file @
e2bff0aa
...
...
@@ -91,6 +91,9 @@ class AlignBox
string
ref_label
;
string
ref
;
/* Marked position, for Cys104 and Phe118/Trp118 */
int
marked_pos
;
/* Identifiers and scores of other possible reference sequence */
vector
<
pair
<
int
,
int
>
>
score
;
};
...
...
Mathieu Giraud
@magiraud
mentioned in issue
#2138 (closed)
·
May 19, 2020
mentioned in issue
#2138 (closed)
mentioned in issue #2138
Toggle commit list
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