Commit d73898be authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: bikeshed strings

parent 11c7f2ba
......@@ -272,9 +272,9 @@ int main (int argc, char **argv)
string cmd = COMMAND_CLONES;
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_DETECT " \t locus detection"
"\n \t\t" COMMAND_CLONES " \t locus/V(D)J detection, window extraction, clone clustering (default command, most efficient, all outputs)"
"\n \t\t" COMMAND_WINDOWS " \t locus/V(D)J detection, window extraction"
"\n \t\t" COMMAND_DETECT " \t locus/V(D)J detection"
"\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) -> type_name("COMMAND");
......@@ -815,9 +815,11 @@ int main (int argc, char **argv)
switch(command) {
case CMD_DETECT: cout << "Detecting V(D)J recombinations" << endl;
break;
case CMD_CLONES: cout << "Analysing clones" << endl;
case CMD_WINDOWS: cout << "Detecting V(D)J recombinations and extracting windows" << endl;
break;
case CMD_SEGMENT: cout << "Segmenting V(D)J" << endl;
case CMD_CLONES: cout << "Detecting V(D)J recombinations and analyzing clones" << endl;
break;
case CMD_SEGMENT: cout << "Designating V(D)J recombinations" << endl;
break;
case CMD_GERMLINES: cout << "Discovering germlines" << endl;
break;
......@@ -1138,12 +1140,12 @@ int main (int argc, char **argv)
//$$ Kmer Segmentation
cout << endl;
cout << "Loop through reads, ";
cout << "Loop through reads, detecting V(D)J recombinations";
if (wmer_size != NO_LIMIT_VALUE)
cout << "looking for windows up to " << wmer_size << "bp" << endl;
cout << " while extracting windows up to " << wmer_size << "bp" << endl;
else
cout << "considering all analyzed reads as windows" << endl;
cout << " while considering all detected reads as windows" << endl;
ofstream *out_segmented = NULL;
ofstream *out_unsegmented = NULL;
......
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