Commit 2a098ac3 authored by Mathieu Giraud's avatar Mathieu Giraud

algo/vidjil.cpp: CMD_SEGMENT is now '-c designations', more balanced help and warn messages

See #3772.
parent 1e13b968
......@@ -87,7 +87,7 @@
#define COMMAND_WINDOWS "windows"
#define COMMAND_CLONES "clones"
#define COMMAND_SEGMENT "segment"
#define COMMAND_SEGMENT "designations"
#define COMMAND_GERMLINES "germlines"
enum { CMD_WINDOWS, CMD_CLONES, CMD_SEGMENT, CMD_GERMLINES } ;
......@@ -150,14 +150,14 @@ string usage_examples(char *progname)
stringstream ss;
ss
<< "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
<< " # including unexpected recombinations (-2), assign V(D)J genes and try to detect the CDR3s (-3))" << endl
<< " " << progname << " -c clones -g germline/homo-sapiens.g:IGH -3 demo/Stanford_S22.fasta # (restrict to complete recombinations on the IGH locus)" << endl
<< " " << progname << " -c clones -g germline/homo-sapiens.g -2 -3 -z 20 demo/LIL-L4.fastq.gz # (basic usage, output detailed V(D)J analysis on the first 20 clones)" << endl
<< " " << progname << " -c windows -g germline/homo-sapiens.g -y 0 -uu -U demo/LIL-L4.fastq.gz # (splits all the reads into (large) files depending on the detection of V(D)J recombinations)" << endl
<< " " << progname << " -c segment -g germline/homo-sapiens.g -2 -3 -X 50 demo/Stanford_S22.fasta # (full analysis of each read, only for debug/testing, here on 50 sampled reads)" << endl
<< " " << progname << " -c germlines -g germline/homo-sapiens.g demo/Stanford_S22.fasta # (statistics on the k-mers)" << endl
<< " " << progname << " -c clones -g germline/homo-sapiens.g:IGH -3 demo/Stanford_S22.fasta # (restrict to complete recombinations on the IGH locus)" << endl
<< " " << progname << " -c clones -g germline/homo-sapiens.g -2 -3 -z 20 demo/LIL-L4.fastq.gz # (basic usage, output detailed V(D)J analysis on the first 20 clones)" << endl
<< " " << progname << " -c windows -g germline/homo-sapiens.g -y 0 -uu -U demo/LIL-L4.fastq.gz # (splits all the reads into (large) files depending on the detection of V(D)J recombinations)" << endl
<< " " << progname << " -c designations -g germline/homo-sapiens.g -2 -3 -X 50 demo/Stanford_S22.fasta # (full analysis of each read, here on 50 sampled reads)" << endl
<< " " << progname << " -c germlines -g germline/homo-sapiens.g demo/Stanford_S22.fasta # (statistics on the k-mers)" << endl
;
return ss.str();
......@@ -252,7 +252,7 @@ int main (int argc, char **argv)
app.add_option("-c", cmd, "command"
"\n \t\t" COMMAND_CLONES " \t locus detection, window extraction, clone clustering (default command, most efficient, all outputs)"
"\n \t\t" COMMAND_WINDOWS " \t locus detection, window extraction"
"\n \t\t" COMMAND_SEGMENT " \t detailed V(D)J designation (not recommended)"
"\n \t\t" COMMAND_SEGMENT " \t detailed V(D)J designation, without prior clustering (not as efficient)"
"\n \t\t" COMMAND_GERMLINES " \t statistics on k-mers in different germlines")
-> group(group) -> set_type_name("COMMAND");
......@@ -739,15 +739,15 @@ int main (int argc, char **argv)
if (command == CMD_SEGMENT)
{
cout << endl
<< "* WARNING: " << PROGNAME << " was run with '-c segment' option" << endl ;
<< "* WARNING: " << PROGNAME << " was run with '-c" COMMAND_SEGMENT "' option" << endl ;
}
if (max_clones == NO_LIMIT_VALUE || max_clones > WARN_MAX_CLONES || command == CMD_SEGMENT)
{
cout << "* " << PROGNAME << " efficientl extracts windows overlapping the CDR3" << endl
cout << "* " << PROGNAME << " efficiently extracts windows overlapping the CDR3" << 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
<< "* is slow and should be done only on small datasets or for testing purposes." << endl
<< "* Computing accurate V(D)J designations for many sequences ('-c " COMMAND_SEGMENT "' or large '-z' values)" << endl
<< "* is not as efficient as the default '-c " COMMAND_CLONES "' command." << endl
<< "* More information is provided in " DOCUMENTATION "." << endl
<< endl ;
}
......@@ -1567,7 +1567,7 @@ int main (int argc, char **argv)
} else if (command == CMD_SEGMENT) {
//$$ CMD_SEGMENT
////////////////////////////////////////
// V(D)J SEGMENTATION //
// V(D)J DESIGNATION //
////////////////////////////////////////
int nb = 0;
......
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