@@ -566,7 +567,7 @@ int main (int argc, char **argv)
->group(group);
booloutput_sequences_by_cluster=false;
app.add_flag("--out-reads",output_sequences_by_cluster,"output all reads by clones ("CLONE_FILENAME"*), to be used only on small datasets")->group(group);
app.add_flag("--out-reads",output_sequences_by_cluster,"output all reads by clones (in "CLONE_DIR"/"CLONE_FILENAME"* files), to be used only on small datasets")->group(group);
booloutput_affects=false;
app.add_flag("--out-affects,-K",output_affects,
...
...
@@ -586,6 +587,16 @@ int main (int argc, char **argv)
boolout_gz=false;
app.add_flag("--gz",out_gz,"output compressed .tsv.gz, .vdj.fa.gz, and .vidjil.gz files")->group(group)->level();
booloutput_vdjfa=false;
app.add_flag("--out-vdjfa",output_vdjfa,
"output clones in a "CLONES_FILENAME" file (only for clone sequence data)")