<<" "<<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
;
returnss.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"