<<" -M <int> maximal admissible delta between last V and first J k-mer (default: "<<DEFAULT_DELTA_MAX<<") (default with -D: "<<DEFAULT_DELTA_MAX_D<<")"<<endl
<<" -w <int> w-mer size used for the length of the extracted window (default: "<<DEFAULT_W<<")"<<endl
<<" -e <float> maximal e-value for determining if a segmentation can be trusted (default: "<<THRESHOLD_NB_EXPECTED<<")"<<endl
<<" -t <int> trim V and J genes (resp. 5' and 3' regions) to keep at most <int> nt (default: "<<DEFAULT_TRIM<<") (0: no trim)"<<endl
<<endl
<<"Labeled windows (these windows will be kept even if -r/-% thresholds are not reached)"<<endl
...
...
@@ -316,6 +319,7 @@ int main (int argc, char **argv)
// Admissible delta between left and right segmentation points
intdelta_min=DEFAULT_DELTA_MIN;// Kmer+Fine
intdelta_max=DEFAULT_DELTA_MAX;// Fine
inttrim_sequences=DEFAULT_TRIM;
booloutput_sequences_by_cluster=false;
booloutput_segmented=false;
...
...
@@ -348,7 +352,7 @@ int main (int argc, char **argv)