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vidjil
vidjil
Commits
dfd8ef75
Commit
dfd8ef75
authored
Feb 27, 2016
by
Mathieu Giraud
Browse files
core/germline.{h,cpp}: mark Cys104 and Phe118/Trp118 from gapped V/J sequences
parent
985b62fa
Changes
2
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Inline
Side-by-side
algo/core/germline.cpp
View file @
dfd8ef75
...
...
@@ -44,6 +44,7 @@ Germline::Germline(string _code, char _shortcut,
f_reps_4
.
push_back
(
f_rep_4
);
f_reps_3
.
push_back
(
f_rep_3
);
/// no CYS104_IN_GAPPED_V / PHE118_TRP118_IN_GAPPED_J here ?
rep_5
=
Fasta
(
f_rep_5
,
2
,
"|"
);
rep_4
=
Fasta
(
f_rep_4
,
2
,
"|"
);
rep_3
=
Fasta
(
f_rep_3
,
2
,
"|"
);
...
...
@@ -64,9 +65,9 @@ Germline::Germline(string _code, char _shortcut,
f_reps_4
=
_f_reps_4
;
f_reps_3
=
_f_reps_3
;
rep_5
=
Fasta
(
2
,
"|"
)
;
rep_5
=
Fasta
(
2
,
"|"
,
CYS104_IN_GAPPED_V
);
rep_4
=
Fasta
(
2
,
"|"
)
;
rep_3
=
Fasta
(
2
,
"|"
)
;
rep_3
=
Fasta
(
2
,
"|"
,
PHE118_TRP118_IN_GAPPED_J
);
for
(
list
<
string
>::
const_iterator
it
=
f_reps_5
.
begin
();
it
!=
f_reps_5
.
end
();
++
it
)
rep_5
.
add
(
*
it
);
...
...
@@ -108,9 +109,9 @@ Germline::Germline(string code, char shortcut, string path, json json_recom, int
init
(
code
,
shortcut
,
delta_min
,
max_indexing
);
rep_5
=
Fasta
(
2
,
"|"
)
;
rep_5
=
Fasta
(
2
,
"|"
,
CYS104_IN_GAPPED_V
)
;
rep_4
=
Fasta
(
2
,
"|"
)
;
rep_3
=
Fasta
(
2
,
"|"
)
;
rep_3
=
Fasta
(
2
,
"|"
,
PHE118_TRP118_IN_GAPPED_J
)
;
for
(
json
::
iterator
it
=
json_recom
[
"5"
].
begin
();
it
!=
json_recom
[
"5"
].
end
();
++
it
)
...
...
algo/core/germline.h
View file @
dfd8ef75
...
...
@@ -17,6 +17,12 @@ enum SEGMENTATION_METHODS {
SEG_METHOD_MAX1U
// Pseudo-germline, most frequent kmer affection and unknwon affectation (-4)
}
;
// JUNCTION/CDR3 extraction from gapped V/J sequences
#define CYS104_IN_GAPPED_V 310 // First nucleotide of Cys104
#define PHE118_TRP118_IN_GAPPED_J 38 // Last nucleotide of Phe118/Trp118
using
namespace
std
;
using
json
=
nlohmann
::
json
;
...
...
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