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vidjil
vidjil
Commits
40e85c6f
Commit
40e85c6f
authored
Oct 16, 2014
by
Mathieu Giraud
Browse files
merge - two commits updating the '-g' option
parents
8fb9d286
7ca20a8d
Changes
3
Hide whitespace changes
Inline
Side-by-side
algo/core/germline.cpp
View file @
40e85c6f
...
...
@@ -109,10 +109,10 @@ void MultiGermline::insert(Germline *germline)
germlines
.
push_back
(
germline
);
}
void
MultiGermline
::
load_default_set
()
void
MultiGermline
::
load_default_set
(
string
path
)
{
germlines
.
push_back
(
new
Germline
(
"TRG"
,
'G'
,
"germline
/TRGV.fa"
,
""
,
"germline
/TRGJ.fa"
,
"#####-#####"
,
-
10
,
20
));
germlines
.
push_back
(
new
Germline
(
"IGH"
,
'H'
,
"germline
/IGHV.fa"
,
"germline
/IGHD.fa"
,
"germline
/IGHJ.fa"
,
"######-######"
,
0
,
80
));
germlines
.
push_back
(
new
Germline
(
"TRG"
,
'G'
,
path
+
"
/TRGV.fa"
,
""
,
path
+
"
/TRGJ.fa"
,
"#####-#####"
,
-
10
,
20
));
germlines
.
push_back
(
new
Germline
(
"IGH"
,
'H'
,
path
+
"
/IGHV.fa"
,
path
+
"
/IGHD.fa"
,
path
+
"
/IGHJ.fa"
,
"######-######"
,
0
,
80
));
}
...
...
algo/core/germline.h
View file @
40e85c6f
...
...
@@ -68,7 +68,7 @@ class MultiGermline {
~
MultiGermline
();
void
insert
(
Germline
*
germline
);
void
load_default_set
();
void
load_default_set
(
string
path
);
void
out_stats
(
ostream
&
out
);
};
...
...
algo/vidjil.cpp
View file @
40e85c6f
...
...
@@ -147,7 +147,7 @@ void usage(char *progname)
<<
" -D <file> D germline multi-fasta file (automatically implies -d)"
<<
endl
<<
" -J <file> J germline multi-fasta file"
<<
endl
<<
" -G <prefix> prefix for V (D) and J repertoires (shortcut for -V <prefix>V.fa -D <prefix>D.fa -J <prefix>J.fa)"
<<
endl
<<
" -g
multiple germlines (experimental)"
<<
endl
<<
" -g
<path>
multiple germlines (experimental)"
<<
endl
<<
endl
<<
"Window prediction"
<<
endl
...
...
@@ -279,6 +279,7 @@ int main (int argc, char **argv)
bool
output_segmented
=
false
;
bool
output_unsegmented
=
false
;
bool
multi_germline
=
false
;
string
multi_germline_file
=
""
;
string
forced_edges
=
""
;
...
...
@@ -294,7 +295,7 @@ int main (int argc, char **argv)
//$$ options: getopt
while
((
c
=
getopt
(
argc
,
argv
,
"AhagG:V:D:J:k:r:vw:e:C:t:l:dc:m:M:N:s:p:Sn:o:L%:Z:y:z:uU"
))
!=
EOF
)
while
((
c
=
getopt
(
argc
,
argv
,
"Ahag
:
G:V:D:J:k:r:vw:e:C:t:l:dc:m:M:N:s:p:Sn:o:L%:Z:y:z:uU"
))
!=
EOF
)
switch
(
c
)
{
...
...
@@ -355,7 +356,8 @@ int main (int argc, char **argv)
break
;
case
'g'
:
multi_germline
=
true
;
multi_germline
=
true
;
multi_germline_file
=
string
(
optarg
);
break
;
case
'G'
:
...
...
@@ -747,9 +749,6 @@ int main (int argc, char **argv)
if
(
!
segment_D
)
// TODO: add other constructor to Fasta, and do not load rep_D in this case
f_rep_D
=
""
;
Fasta
rep_V
(
f_rep_V
,
2
,
"|"
,
cout
);
Fasta
rep_D
(
f_rep_D
,
2
,
"|"
,
cout
);
Fasta
rep_J
(
f_rep_J
,
2
,
"|"
,
cout
);
OnlineFasta
*
reads
;
...
...
@@ -785,10 +784,14 @@ int main (int argc, char **argv)
if
(
multi_germline
)
{
multigermline
->
load_default_set
();
multigermline
->
load_default_set
(
multi_germline_file
);
}
else
{
Fasta
rep_V
(
f_rep_V
,
2
,
"|"
,
cout
);
Fasta
rep_D
(
f_rep_D
,
2
,
"|"
,
cout
);
Fasta
rep_J
(
f_rep_J
,
2
,
"|"
,
cout
);
Germline
*
germline
;
germline
=
new
Germline
(
germline_system
,
'X'
,
rep_V
,
rep_D
,
rep_J
,
seed
,
...
...
@@ -1309,6 +1312,11 @@ int main (int argc, char **argv)
<<
"* They should be checked with other softwares such as IgBlast, iHHMune-align or IMGT/V-QUEST."
<<
endl
;
Fasta
rep_V
(
f_rep_V
,
2
,
"|"
,
cout
);
Fasta
rep_D
(
f_rep_D
,
2
,
"|"
,
cout
);
Fasta
rep_J
(
f_rep_J
,
2
,
"|"
,
cout
);
Germline
*
germline
;
// Here, it could be run without building the index
...
...
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