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vidjil
vidjil
Commits
c06c7fc2
Commit
c06c7fc2
authored
Mar 11, 2019
by
Mathieu Giraud
Browse files
vidjil.cpp: --grep-reads combo
Bye-bye -FaW, see
#3785
.
parent
d232fc28
Changes
1
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Inline
Side-by-side
algo/vidjil.cpp
View file @
c06c7fc2
...
...
@@ -569,6 +569,20 @@ int main (int argc, char **argv)
bool
__only_on_exit__clean_memory
;
// Do not use except on exit, see #3729
app
.
add_flag
(
"--clean-memory"
,
__only_on_exit__clean_memory
,
"clean memory on exit"
)
->
group
(
group
)
->
level
();
// ----------------------------------------------------------------------------------------------------------------------
group
=
"Presets"
;
app
.
add_option
(
"--grep-reads"
,
[
&
only_labeled_windows
,
&
windows_labels_explicit
,
&
output_sequences_by_cluster
](
CLI
::
results_t
res
)
{
only_labeled_windows
=
true
;
windows_labels_explicit
.
push_back
(
res
[
0
].
c_str
());
output_sequences_by_cluster
=
true
;
return
true
;
},
"output, by clone, reads related to the given window sequence, even when they are below the thresholds"
PAD_HELP
"(equivalent to --label SEQUENCE -label-filter --out-reads)"
)
->
group
(
group
)
->
level
()
->
set_type_name
(
"SEQUENCE"
);
// ----------------------------------------------------------------------------------------------------------------------
group
=
"Help"
;
app
.
set_help_flag
(
"--help,-h"
,
"help"
)
...
...
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