Commit ee010248 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: define and use DOCUMENTATION

parent ee596525
...@@ -70,6 +70,7 @@ ...@@ -70,6 +70,7 @@
#define PROGNAME "vidjil-algo" #define PROGNAME "vidjil-algo"
#define VIDJIL_JSON_VERSION "2016b" #define VIDJIL_JSON_VERSION "2016b"
#define DOCUMENTATION "doc/vidjil-algo.md"
//$$ #define (mainly default options) //$$ #define (mainly default options)
...@@ -148,7 +149,7 @@ string usage_examples(char *progname) ...@@ -148,7 +149,7 @@ string usage_examples(char *progname)
{ {
stringstream ss; stringstream ss;
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 << " " << 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 << " # 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 << " # 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) ...@@ -571,7 +572,7 @@ int main (int argc, char **argv)
app.add_flag_function("-H", [&](size_t n) { UNUSED(n); throw CLI::CallForAdvancedHelp() ; }, app.add_flag_function("-H", [&](size_t n) { UNUSED(n); throw CLI::CallForAdvancedHelp() ; },
"help, including advanced and experimental options" "help, including advanced and experimental options"
"\n " "\n "
"The full help is available in the doc/algo.org file.") "The full help is available in " DOCUMENTATION ".")
-> group(group); -> group(group);
...@@ -749,7 +750,7 @@ int main (int argc, char **argv) ...@@ -749,7 +750,7 @@ int main (int argc, char **argv)
<< "* to cluster reads into clones ('-c clones')." << endl << "* to cluster reads into clones ('-c clones')." << endl
<< "* Computing accurate V(D)J designations for many sequences ('-c segment' or large '-z' values)" << 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 << "* 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 ; << endl ;
} }
...@@ -1095,7 +1096,7 @@ int main (int argc, char **argv) ...@@ -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); 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 << " ! 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); we.out_stats(stream_segmentation_info);
......
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