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vidjil
vidjil
Commits
9e7678b9
Commit
9e7678b9
authored
Oct 14, 2014
by
Marc Duez
Browse files
c++ : vidjil.cpp : update json output to 2014.10.10 format
parent
088b5f02
Changes
1
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Inline
Side-by-side
algo/vidjil.cpp
View file @
9e7678b9
...
...
@@ -463,6 +463,12 @@ int main (int argc, char **argv)
output_segmented
=
true
;
break
;
}
//remove germline path
string
tmp_germline_system
;
stringstream
stream
(
germline_system
);
while
(
getline
(
stream
,
tmp_germline_system
,
'/'
)
)
germline_system
=
tmp_germline_system
;
// If there was no -w option, then w is either DEFAULT_W or DEFAULT_W_D
if
(
w
==
0
)
...
...
@@ -1221,33 +1227,60 @@ int main (int argc, char **argv)
JsonArray
json_nb_segmented
;
json_nb_segmented
.
add
(
nb_segmented
);
JsonArray
json_original_names
;
json_original_names
.
add
(
f_reads
);
JsonArray
json_timestamp
;
json_timestamp
.
add
(
time_buffer
);
JsonArray
json_log
;
json_log
.
add
(
stream_segmentation_info
.
str
());
JsonArray
json_cmdline
;
json_cmdline
.
add
(
stream_cmdline
.
str
());
// TODO: escape "s in argv
JsonArray
jsonSortedWindows
=
windowsStorage
->
sortedWindowsToJsonArray
(
json_data_segment
,
norm_list
,
nb_segmented
);
//samples field
JsonList
*
json_samples
;
json_samples
=
new
JsonList
();
json_samples
->
add
(
"number"
,
"1"
);
JsonArray
json_original_names
;
json_original_names
.
add
(
f_reads
);
json_samples
->
add
(
"number"
,
1
);
json_samples
->
add
(
"original_names"
,
json_original_names
);
json_samples
->
add
(
"timestamp"
,
json_timestamp
);
json_samples
->
add
(
"log"
,
json_log
);
json_samples
->
add
(
"commandline"
,
json_cmdline
);
//reads field
JsonList
*
json_reads
;
json_reads
=
new
JsonList
();
json_reads
->
add
(
"total"
,
json_nb_reads
);
json_reads
->
add
(
"segmented"
,
json_nb_segmented
);
JsonList
*
json_reads_germlineList
;
json_reads_germlineList
=
new
JsonList
();
if
(
multi_germline
)
{
for
(
list
<
Germline
*>::
const_iterator
it
=
multigermline
->
germlines
.
begin
();
it
!=
multigermline
->
germlines
.
end
();
++
it
)
{
Germline
*
germline
=
*
it
;
JsonArray
json_reads_germline
;
json_reads_germline
.
add
(
we
.
getNbReadsGermline
(
germline
->
code
));
json_reads_germlineList
->
add
(
germline
->
code
,
json_reads_germline
);
}
}
else
{
json_reads_germlineList
->
add
(
germline_system
,
json_nb_segmented
);
}
json_reads
->
add
(
"germline"
,
*
json_reads_germlineList
);
json
->
add
(
"vidjil_json_version"
,
VIDJIL_JSON_VERSION
);
json
->
add
(
"samples"
,
*
json_samples
);
json
->
add
(
"timestamp"
,
json_timestamp
);
json
->
add
(
"commandline"
,
stream_cmdline
.
str
());
// TODO: escape "s in argv
json
->
add
(
"segmentation_info"
,
stream_segmentation_info
.
str
());
json
->
add
(
"reads"
,
*
json_reads
);
json
->
add
(
"germline"
,
germline_system
);
json
->
add
(
"germline_V"
,
f_rep_V
);
json
->
add
(
"germline_J"
,
f_rep_J
);
json
->
add
(
"reads_total"
,
json_nb_reads
);
json
->
add
(
"reads_segmented"
,
json_nb_segmented
);
json
->
add
(
"windows"
,
jsonSortedWindows
);
json
->
add
(
"clones"
,
jsonSortedWindows
);
//Added edges in the json output file
//json->add("links", jsonLevenshtein);
...
...
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