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vidjil
vidjil
Commits
29d11583
Commit
29d11583
authored
Oct 14, 2018
by
Mathieu Giraud
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vidjil.cpp: remove json_data_segment and use windowsStorage->sortedWindowsToOutput()
See
#3358
.
parent
d856b56f
Changes
1
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algo/vidjil.cpp
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algo/vidjil.cpp
View file @
29d11583
...
...
@@ -1089,8 +1089,6 @@ int main (int argc, char **argv)
we
.
out_stats
(
stream_segmentation_info
);
cout
<<
stream_segmentation_info
.
str
();
map
<
junction
,
json
>
json_data_segment
;
//////////////////////////////////
//$$ Sort windows
...
...
@@ -1333,6 +1331,7 @@ int main (int argc, char **argv)
CloneOutput
*
clone
=
new
CloneOutput
();
output
->
addClone
(
it
->
first
,
clone
);
clone
->
set
(
"sequence"
,
kseg
->
getSequence
().
sequence
);
clone
->
set
(
"_coverage"
,
{
repComp
.
getCoverage
()
});
clone
->
set
(
"_average_read_length"
,
{
windowsStorage
->
getAverageLength
(
it
->
first
)
});
...
...
@@ -1361,7 +1360,6 @@ int main (int argc, char **argv)
{
cout
<<
representative
<<
endl
;
out_clones
<<
representative
<<
endl
;
json_data_segment
[
it
->
first
]
=
clone
.
toJson
();
continue
;
}
...
...
@@ -1425,9 +1423,7 @@ int main (int argc, char **argv)
out_clone
<<
endl
;
}
// end if (seg.isSegmented())
seg
.
checkWarnings
(
clone
);
json_data_segment
[
it
->
first
]
=
clone
.
toJson
();
if
(
output_sequences_by_cluster
)
// -a option, output all sequences
{
...
...
@@ -1485,7 +1481,7 @@ int main (int argc, char **argv)
}
// end if (command == CMD_CLONES)
//$$ .json output
: json_data_segment
//$$ .json output
cout
<<
endl
;
//json custom germline
...
...
@@ -1514,7 +1510,7 @@ int main (int argc, char **argv)
//out_json << json->toString();
windowsStorage
->
clearSequences
();
json
jsonSortedWindows
=
windowsStorage
->
sortedWindowsTo
Json
(
json_data_segmen
t
,
max_clones_id
);
windowsStorage
->
sortedWindowsTo
Output
(
outpu
t
,
max_clones_id
);
json
reads_germline
;
for
(
list
<
Germline
*>::
const_iterator
it
=
multigermline
->
germlines
.
begin
();
it
!=
multigermline
->
germlines
.
end
();
++
it
){
...
...
@@ -1531,9 +1527,7 @@ int main (int argc, char **argv)
{
"segmented"
,
{
nb_segmented
}},
{
"germline"
,
reads_germline
}
});
output
->
set
(
"clones"
,
jsonSortedWindows
);
output
->
set
(
"germlines"
,
json_germlines
);
output
->
set
(
"germlines"
,
"ref"
,
multigermline
->
ref
);
output
->
set
(
"germlines"
,
"species"
,
multigermline
->
species
)
;
output
->
set
(
"germlines"
,
"species_taxon_id"
,
multigermline
->
species_taxon_id
)
;
...
...
@@ -1589,6 +1583,7 @@ int main (int argc, char **argv)
FineSegmenter
s
(
seq
,
germline
,
segment_cost
,
expected_value
,
nb_reads_for_evalue
,
kmer_threshold
,
alternative_genes
);
CloneOutput
*
clone
=
new
CloneOutput
();
output
->
addClone
(
seq
.
label
,
clone
);
clone
->
set
(
"id"
,
seq
.
label
);
clone
->
set
(
"sequence"
,
seq
.
sequence
);
clone
->
set
(
"reads"
,
{
1
});
...
...
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