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vidjil
vidjil
Commits
e758a07c
Commit
e758a07c
authored
Apr 28, 2020
by
Mathieu Giraud
Browse files
vidjil.cpp: --gz also outputs AIRR .tsv.gz
see
#4269
parent
13375bc1
Changes
1
Hide whitespace changes
Inline
Side-by-side
algo/vidjil.cpp
View file @
e758a07c
...
...
@@ -584,7 +584,7 @@ int main (int argc, char **argv)
app
.
add_option
(
"--base,-b"
,
f_basename
,
"output basename (by default basename of the input file)"
)
->
group
(
group
)
->
type_name
(
"STRING"
);
bool
out_gz
=
false
;
app
.
add_flag
(
"--gz"
,
out_gz
,
"output compressed .vidjil.gz file"
)
->
group
(
group
)
->
level
();
app
.
add_flag
(
"--gz"
,
out_gz
,
"output compressed
.tsv.gz and
.vidjil.gz file
s
"
)
->
group
(
group
)
->
level
();
bool
no_airr
=
false
;
bool
no_vidjil
=
false
;
...
...
@@ -825,7 +825,10 @@ int main (int argc, char **argv)
string
f_json
=
out_dir
+
f_basename
+
JSON_SUFFIX
;
if
(
out_gz
)
{
f_airr
+=
GZ_SUFFIX
;
f_json
+=
GZ_SUFFIX
;
}
ostringstream
stream_cmdline
;
for
(
int
i
=
0
;
i
<
argc
;
i
++
)
stream_cmdline
<<
argv
[
i
]
<<
" "
;
...
...
@@ -1744,12 +1747,13 @@ int main (int argc, char **argv)
cout
<<
endl
;
}
//$ Output AIRR .tsv
//$ Output AIRR .tsv
(.gz)
if
(
!
no_airr
)
{
cout
<<
" ==> "
<<
f_airr
<<
"
\t
(AIRR output)"
<<
endl
;
ofstream
out_airr
(
f_airr
.
c_str
());
static_cast
<
SampleOutputAIRR
*>
(
&
output
)
->
out
(
out_airr
);
std
::
ostream
*
out_airr
=
new_ofgzstream
(
f_airr
.
c_str
(),
out_gz
);
static_cast
<
SampleOutputAIRR
*>
(
&
output
)
->
out
(
*
out_airr
);
delete
out_airr
;
}
//$ Output .vidjil(.gz) json
...
...
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