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vidjil
vidjil
Commits
d0c3b05a
Commit
d0c3b05a
authored
Feb 28, 2016
by
Mathieu Giraud
Browse files
core/segment.{h,cpp}: compute and store CDR3nuc, CDR3aa, JUNCTIONaa
parent
e0bbf0d2
Changes
2
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Inline
Side-by-side
algo/core/segment.cpp
View file @
d0c3b05a
...
...
@@ -1057,6 +1057,12 @@ void FineSegmenter::findCDR3(){
// IMGT-CDR3 is, on each side, 3 nucleotides shorter than IMGT-JUNCTION
CDR3start
=
JUNCTIONstart
+
3
;
CDR3end
=
JUNCTIONend
-
3
;
CDR3nuc
=
subsequence
(
getSequence
().
sequence
,
CDR3start
,
CDR3end
);
CDR3aa
=
nuc_to_aa
(
CDR3nuc
);
JUNCTIONaa
=
nuc_to_aa
(
subsequence
(
getSequence
().
sequence
,
JUNCTIONstart
,
CDR3start
-
1
))
+
CDR3aa
+
nuc_to_aa
(
subsequence
(
getSequence
().
sequence
,
CDR3end
+
1
,
JUNCTIONend
));
}
json
FineSegmenter
::
toJson
(){
...
...
algo/core/segment.h
View file @
d0c3b05a
...
...
@@ -121,7 +121,11 @@ protected:
string
sequence_or_rc
;
int
JUNCTIONstart
,
JUNCTIONend
;
string
JUNCTIONaa
;
int
CDR3start
,
CDR3end
;
string
CDR3nuc
;
string
CDR3aa
;
bool
reversed
,
segmented
,
dSegmented
;
int
because
;
...
...
Mathieu Giraud
@magiraud
mentioned in issue
#2428 (closed)
·
May 11, 2017
mentioned in issue
#2428 (closed)
mentioned in issue #2428
Toggle commit list
Mathieu Giraud
@magiraud
mentioned in issue
#2434
·
May 11, 2017
mentioned in issue
#2434
mentioned in issue #2434
Toggle commit list
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