Commit 2b5c51be authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: help, update

parent d60c0084
...@@ -123,7 +123,7 @@ enum { CMD_WINDOWS, CMD_CLONES, CMD_SEGMENT, CMD_GERMLINES } ; ...@@ -123,7 +123,7 @@ enum { CMD_WINDOWS, CMD_CLONES, CMD_SEGMENT, CMD_GERMLINES } ;
#define MAX_CLONES_FOR_SIMILARITY 20 #define MAX_CLONES_FOR_SIMILARITY 20
// warn // warn
#define WARN_MAX_CLONES 100 #define WARN_MAX_CLONES 5000
#define WARN_PERCENT_SEGMENTED 40 #define WARN_PERCENT_SEGMENTED 40
#define WARN_COVERAGE 0.6 #define WARN_COVERAGE 0.6
#define WARN_NUM_CLONES_SIMILAR 10 #define WARN_NUM_CLONES_SIMILAR 10
...@@ -252,7 +252,7 @@ int main (int argc, char **argv) ...@@ -252,7 +252,7 @@ int main (int argc, char **argv)
// ---------------------------------------------------------------------------------------------------------------------- // ----------------------------------------------------------------------------------------------------------------------
group = "Germline presets (at least one -g or -V/(-D)/-J option must be given for all commands except -c " COMMAND_GERMLINES ")"; group = "Germline presets (at least one -g or -V/(-D)/-J option must be given)";
vector <string> multi_germlines ; vector <string> multi_germlines ;
app.add_option("-g", multi_germlines, R"Z( app.add_option("-g", multi_germlines, R"Z(
...@@ -262,7 +262,7 @@ int main (int argc, char **argv) ...@@ -262,7 +262,7 @@ int main (int argc, char **argv)
The list of locus/recombinations can be restricted, such as in '-g germline/homo-sapiens.g:IGH,IGK,IGL' The list of locus/recombinations can be restricted, such as in '-g germline/homo-sapiens.g:IGH,IGK,IGL'
-g PATH -g PATH
multiple locus/germlines, shortcut for '-g PATH/)Z" DEFAULT_MULTI_GERMLINE_FILE R"Z(', multiple locus/germlines, shortcut for '-g PATH/)Z" DEFAULT_MULTI_GERMLINE_FILE R"Z(',
processes human TRA, TRB, TRG, TRD, IGH, IGK and IGL locus, possibly with some incomplete/unusal recombination)Z") processes human TRA, TRB, TRG, TRD, IGH, IGK and IGL locus, possibly with some incomplete/unusal recombinations)Z")
-> group(group) -> set_type_name("GERMLINES"); -> group(group) -> set_type_name("GERMLINES");
vector <string> v_reps_V ; vector <string> v_reps_V ;
...@@ -275,7 +275,7 @@ int main (int argc, char **argv) ...@@ -275,7 +275,7 @@ int main (int argc, char **argv)
app.add_option("-D", v_reps_D, app.add_option("-D", v_reps_D,
"custom D germline multi-fasta file(s) (and resets -m and -w options), will segment into V(D)J components") "custom D germline multi-fasta file(s), segment into V(D)J components")
-> group(group) -> set_type_name("FILE"); -> group(group) -> set_type_name("FILE");
app.add_option("-J", v_reps_J, app.add_option("-J", v_reps_J,
...@@ -353,7 +353,7 @@ int main (int argc, char **argv) ...@@ -353,7 +353,7 @@ int main (int argc, char **argv)
seed_changed = true; seed_changed = true;
return true; return true;
}, },
"seed, possibly spaced, used for the V/J affectation (default: depends on germline), given either explicitely, either by an alias" "seed, possibly spaced, used for the V/J affectation (default: depends on germline), given either explicitely or by an alias"
"\n " + string_of_map(seedMap, " ") "\n " + string_of_map(seedMap, " ")
) )
-> group(group) -> level() -> set_type_name("SEED=" DEFAULT_SEED); -> group(group) -> level() -> set_type_name("SEED=" DEFAULT_SEED);
...@@ -734,7 +734,7 @@ int main (int argc, char **argv) ...@@ -734,7 +734,7 @@ 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/algo.org' file." << endl << "* More information is provided in the 'doc/vidjil-algo.md' file." << endl
<< endl ; << endl ;
} }
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment