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vidjil
vidjil
Commits
94fa2a42
Commit
94fa2a42
authored
Feb 02, 2017
by
Mathieu Giraud
Browse files
vidjil.cpp, core/germline.{h,c}: remove (in)complete filtering mechanism that was used with -i.
This should fix
#2153
.
parent
a51e62a3
Changes
3
Hide whitespace changes
Inline
Side-by-side
algo/core/germline.cpp
View file @
94fa2a42
...
...
@@ -256,7 +256,7 @@ void MultiGermline::add_germline(Germline *germline)
germlines
.
push_back
(
germline
);
}
void
MultiGermline
::
build_from_json
(
string
path
,
string
json_filename_and_filter
,
int
filter
,
int
max_indexing
)
void
MultiGermline
::
build_from_json
(
string
path
,
string
json_filename_and_filter
,
int
max_indexing
)
{
//extract json_filename and systems_filter
...
...
@@ -309,19 +309,6 @@ void MultiGermline::build_from_json(string path, string json_filename_and_filter
continue
;
}
switch
(
filter
)
{
case
GERMLINES_REGULAR
:
if
(
code
.
find
(
"+"
)
!=
string
::
npos
)
continue
;
break
;
case
GERMLINES_INCOMPLETE
:
if
(
code
.
find
(
"+"
)
==
string
::
npos
)
continue
;
break
;
default:
break
;
}
map
<
string
,
string
>
seedMap
;
seedMap
[
"13s"
]
=
SEED_S13
;
seedMap
[
"12s"
]
=
SEED_S12
;
...
...
algo/core/germline.h
View file @
94fa2a42
...
...
@@ -119,11 +119,6 @@ class Germline {
ostream
&
operator
<<
(
ostream
&
out
,
const
Germline
&
germline
);
enum
GERMLINES_FILTER
{
GERMLINES_ALL
,
GERMLINES_REGULAR
,
GERMLINES_INCOMPLETE
}
;
class
MultiGermline
{
private:
IndexTypes
indexType
;
...
...
@@ -147,10 +142,9 @@ class MultiGermline {
* Build from a json .g germline file
* path: path, such as 'germline/'
* json_filename_and_filter: filename, optionally embedding a filter, such as 'homo-sapiens.g:IGH,TRG'
* filter: see GERMLINES_FILTER
* max_indexing:
*/
void
build_from_json
(
string
path
,
string
json_filename_and_filter
,
int
filter
,
int
max_indexing
);
void
build_from_json
(
string
path
,
string
json_filename_and_filter
,
int
max_indexing
);
/**
* Finishes the construction of the multi germline so that it can be used
...
...
algo/vidjil.cpp
View file @
94fa2a42
...
...
@@ -849,7 +849,7 @@ int main (int argc, char **argv)
for
(
pair
<
string
,
string
>
path_file
:
multi_germline_paths_and_files
)
{
try
{
multigermline
->
build_from_json
(
path_file
.
first
,
path_file
.
second
,
GERMLINES_REGULAR
,
trim_sequences
);
multigermline
->
build_from_json
(
path_file
.
first
,
path_file
.
second
,
trim_sequences
);
}
catch
(
std
::
exception
&
e
)
{
cerr
<<
ERROR_STRING
<<
"Vidjil cannot properly read "
<<
path_file
.
first
<<
"/"
<<
path_file
.
second
<<
": "
<<
e
.
what
()
<<
endl
;
exit
(
1
);
...
...
@@ -897,10 +897,9 @@ int main (int argc, char **argv)
multigermline
->
germlines
.
push_back
(
pseudo_u
);
}
// Should come after the initialization of
regular (and possibly pseudo)
germlines
// Should come after the initialization of
all
germlines
{
for
(
pair
<
string
,
string
>
path_file
:
multi_germline_paths_and_files
)
multigermline
->
build_from_json
(
path_file
.
first
,
path_file
.
second
,
GERMLINES_INCOMPLETE
,
trim_sequences
);
if
((
!
multigermline
->
one_index_per_germline
)
&&
(
command
!=
CMD_GERMLINES
))
{
multigermline
->
insert_in_one_index
(
multigermline
->
index
,
true
);
}
...
...
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