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vidjil
vidjil
Commits
cffcd742
Commit
cffcd742
authored
Dec 03, 2014
by
Mathieu Giraud
Browse files
vidjil.cpp: new experimental option '-i', some incomplete rearrangements
parent
2d9c7ce4
Changes
1
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Inline
Side-by-side
algo/vidjil.cpp
View file @
cffcd742
...
...
@@ -149,6 +149,7 @@ void usage(char *progname)
<<
" -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) (basename gives germline code)"
<<
endl
<<
" -g <path> multiple germlines (in the path <path>, takes TRA, TRB, TRG, TRD, IGH and IGL and sets window prediction parameters)"
<<
endl
<<
" -i multiple germlines, also incomplete rearrangements (experimental, must be used with -g)"
<<
endl
<<
endl
<<
"Window prediction"
<<
endl
...
...
@@ -279,6 +280,7 @@ int main (int argc, char **argv)
bool
output_segmented
=
false
;
bool
output_unsegmented
=
false
;
bool
multi_germline
=
false
;
bool
multi_germline_incomplete
=
false
;
string
multi_germline_file
=
DEFAULT_MULTIGERMLINE
;
string
forced_edges
=
""
;
...
...
@@ -294,7 +296,7 @@ int main (int argc, char **argv)
//$$ options: getopt
while
((
c
=
getopt
(
argc
,
argv
,
"Ahag:G:V:D:J:k:r:vw:e:C:f:l:c:m:M:N:s:b:Sn:o:L%:y:z:uU"
))
!=
EOF
)
while
((
c
=
getopt
(
argc
,
argv
,
"Aha
i
g:G:V:D:J:k:r:vw:e:C:f:l:c:m:M:N:s:b:Sn:o:L%:y:z:uU"
))
!=
EOF
)
switch
(
c
)
{
...
...
@@ -341,7 +343,11 @@ int main (int argc, char **argv)
multi_germline_file
=
string
(
optarg
);
germline_system
=
"multi"
;
break
;
case
'i'
:
multi_germline_incomplete
=
true
;
break
;
case
'G'
:
germline_system
=
string
(
optarg
);
f_reps_V
.
push_back
((
germline_system
+
"V.fa"
).
c_str
())
;
...
...
@@ -676,6 +682,8 @@ int main (int argc, char **argv)
if
(
multi_germline
)
{
multigermline
->
build_default_set
(
multi_germline_file
);
if
(
multi_germline_incomplete
)
multigermline
->
build_incomplete_set
(
multi_germline_file
);
}
else
if
(
command
==
CMD_GERMLINES
)
{
...
...
Vidjil Team
@vidjilteam
Mentioned in issue
#1304 (closed)
·
Nov 29, 2016
Mentioned in issue
#1304 (closed)
Mentioned in issue #1304
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