Commit ba3aa473 authored by Mathieu Giraud's avatar Mathieu Giraud Committed by Mikaël Salson

vidjil.cpp: help on -Z, bikeshed message

parent 0dee5399
......@@ -110,6 +110,8 @@ enum { CMD_WINDOWS, CMD_CLONES, CMD_SEGMENT, CMD_GERMLINES } ;
#define DEFAULT_MAX_AUDITIONED 2000
#define DEFAULT_RATIO_REPRESENTATIVE 0.5
#define DEFAULT_KMER_THRESHOLD NO_LIMIT_VALUE
#define DEFAULT_EPSILON 0
#define DEFAULT_MINPTS 10
......@@ -221,7 +223,7 @@ int usage(char *progname, bool advanced)
cerr << "Fine segmentation options (second pass)" << endl
<< " -f <string> use custom Cost for fine segmenter : format \"match, subst, indels, del_end, homo\" (default "<< DEFAULT_SEGMENT_COST <<" )"<< endl
<< " -E <float> maximal e-value for determining if a D segment can be trusted (default: " << THRESHOLD_NB_EXPECTED_D << ")" << endl
<< " -Z <nb> use custom filter with threshold to reduce calculation time" << endl
<< " -Z <nb> typical number of V genes, selected by k-mer comparison, to compare to the read ('" << NO_LIMIT << "': all genes, default)" << endl
<< endl;
cerr << "Clone analysis (second pass)" << endl
......@@ -398,7 +400,7 @@ int main (int argc, char **argv)
bool jsonLevenshteinComputed = false ;
//the number of k-mer used in filter function
int kmer_threshold = NO_LIMIT_VALUE;
int kmer_threshold = DEFAULT_KMER_THRESHOLD;
//$$ options: getopt
......
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