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vidjil
vidjil
Commits
ee010248
Commit
ee010248
authored
Mar 06, 2019
by
Mathieu Giraud
Browse files
vidjil.cpp: define and use DOCUMENTATION
parent
ee596525
Changes
1
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Side-by-side
algo/vidjil.cpp
View file @
ee010248
...
...
@@ -70,6 +70,7 @@
#define PROGNAME "vidjil-algo"
#define VIDJIL_JSON_VERSION "2016b"
#define DOCUMENTATION "doc/vidjil-algo.md"
//$$ #define (mainly default options)
...
...
@@ -148,7 +149,7 @@ string usage_examples(char *progname)
{
stringstream
ss
;
ss
<<
"Examples (see
doc/algo.org
)"
<<
endl
<<
"Examples (see
"
DOCUMENTATION
"
)"
<<
endl
<<
" "
<<
progname
<<
" -c clones -g germline/homo-sapiens.g -2 -3 -r 1 demo/Demo-X5.fa # (basic usage, detect the locus for each read,"
<<
endl
<<
" # cluster reads and report clones starting from the first read (-r 1),"
<<
endl
<<
" # including unexpected recombinations (-2), assign V(D)J genes and try to detect the CDR3s (-3))"
<<
endl
...
...
@@ -571,7 +572,7 @@ int main (int argc, char **argv)
app
.
add_flag_function
(
"-H"
,
[
&
](
size_t
n
)
{
UNUSED
(
n
);
throw
CLI
::
CallForAdvancedHelp
()
;
},
"help, including advanced and experimental options"
"
\n
"
"The full help is available in
the doc/algo.org file
."
)
"The full help is available in
"
DOCUMENTATION
"
."
)
->
group
(
group
);
...
...
@@ -749,7 +750,7 @@ int main (int argc, char **argv)
<<
"* to cluster reads into clones ('-c clones')."
<<
endl
<<
"* Computing accurate V(D)J designations for many sequences ('-c segment' or large '-z' values)"
<<
endl
<<
"* is slow and should be done only on small datasets or for testing purposes."
<<
endl
<<
"* More information is provided in
the 'doc/vidjil-algo.md' file
."
<<
endl
<<
"* More information is provided in
"
DOCUMENTATION
"
."
<<
endl
<<
endl
;
}
...
...
@@ -1095,7 +1096,7 @@ int main (int argc, char **argv)
{
output
.
add_warning
(
"W20"
,
"Very few V(D)J recombinations found: "
+
fixed_string_of_float
(
ratio_segmented
,
2
)
+
"%"
,
LEVEL_WARN
);
stream_segmentation_info
<<
" ! There are not so many CDR3 windows found in this set of reads."
<<
endl
;
stream_segmentation_info
<<
" ! Please check the
unsegmentation
causes below and refer to
the documentation
."
<<
endl
;
stream_segmentation_info
<<
" ! Please check the causes below and refer to
"
DOCUMENTATION
"
."
<<
endl
;
}
we
.
out_stats
(
stream_segmentation_info
);
...
...
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