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vidjil
vidjil
Commits
e2bff0aa
Commit
e2bff0aa
authored
Feb 29, 2016
by
Mathieu Giraud
Browse files
core/segment.{h,cpp}: remember in AligBox the 'marked_pos' coming from the DP backtrack
parent
6e1d108c
Changes
2
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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
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