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vidjil
vidjil
Commits
0ed84321
Commit
0ed84321
authored
Feb 12, 2021
by
Mathieu Giraud
Browse files
vidjil.cpp: --gz also output *detected.fa.gz files
see
#4692
parent
a95c2ed5
Changes
1
Hide whitespace changes
Inline
Side-by-side
algo/vidjil.cpp
View file @
0ed84321
...
...
@@ -601,7 +601,7 @@ 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 .tsv.gz,
.vdj
.fa.gz, and .vidjil.gz files"
)
->
group
(
group
)
->
level
();
app
.
add_flag
(
"--gz"
,
out_gz
,
"output compressed .tsv.gz, .fa.gz, and .vidjil.gz files"
)
->
group
(
group
)
->
level
();
bool
show_alignments
=
false
;
app
.
add_flag
(
"--show-junction"
,
show_alignments
,
...
...
@@ -1147,9 +1147,9 @@ int main (int argc, char **argv)
else
cout
<<
" while considering all detected reads as windows"
<<
endl
;
o
f
stream
*
out_segmented
=
NULL
;
o
f
stream
*
out_unsegmented
=
NULL
;
o
f
stream
*
out_unsegmented_detail
[
STATS_SIZE
];
ostream
*
out_segmented
=
NULL
;
ostream
*
out_unsegmented
=
NULL
;
ostream
*
out_unsegmented_detail
[
STATS_SIZE
];
ofstream
*
out_affects
=
NULL
;
WindowExtractor
we
(
multigermline
);
...
...
@@ -1158,15 +1158,19 @@ int main (int argc, char **argv)
if
(
output_segmented
)
{
string
f_segmented
=
out_dir
+
f_basename
+
SEGMENTED_FILENAME
;
if
(
out_gz
)
f_segmented
+=
GZ_SUFFIX
;
cout
<<
" ==> "
<<
f_segmented
<<
endl
;
out_segmented
=
new
ofstream
(
f_segmented
.
c_str
());
out_segmented
=
new
_
of
gz
stream
(
f_segmented
.
c_str
()
,
out_gz
);
we
.
setSegmentedOutput
(
out_segmented
);
}
if
(
output_unsegmented
)
{
string
f_unsegmented
=
out_dir
+
f_basename
+
UNSEGMENTED_FILENAME
;
if
(
out_gz
)
f_unsegmented
+=
GZ_SUFFIX
;
cout
<<
" ==> "
<<
f_unsegmented
<<
endl
;
out_unsegmented
=
new
ofstream
(
f_unsegmented
.
c_str
());
out_unsegmented
=
new
_
of
gz
stream
(
f_unsegmented
.
c_str
()
,
out_gz
);
we
.
setUnsegmentedOutput
(
out_unsegmented
);
}
...
...
@@ -1182,8 +1186,10 @@ int main (int argc, char **argv)
replace
(
s
.
begin
(),
s
.
end
(),
'\''
,
'_'
);
string
f_unsegmented_detail
=
out_dir
+
f_basename
+
"."
+
s
+
UNSEGMENTED_DETAIL_FILENAME
;
if
(
out_gz
)
f_unsegmented_detail
+=
GZ_SUFFIX
;
cout
<<
" ==> "
<<
f_unsegmented_detail
<<
endl
;
out_unsegmented_detail
[
i
]
=
new
ofstream
(
f_unsegmented_detail
.
c_str
());
out_unsegmented_detail
[
i
]
=
new
_
of
gz
stream
(
f_unsegmented_detail
.
c_str
()
,
out_gz
);
}
we
.
setUnsegmentedDetailOutput
(
out_unsegmented_detail
,
output_unsegmented_detail_full
);
...
...
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