Commit cd8d1183 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: -h, use default values for costs rather than hard-coded values

parent 2b80952f
......@@ -216,7 +216,7 @@ void usage(char *progname, bool advanced)
if (advanced)
cerr << "Fine segmentation options (second pass)" << endl
<< " -f <string> use custom Cost for fine segmenter : format \"match, subst, indels, homo, del_end\" (default "<<VDJ<<" )"<< endl
<< " -f <string> use custom Cost for fine segmenter : format \"match, subst, indels, homo, del_end\" (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
<< endl ;
......@@ -231,7 +231,7 @@ void usage(char *progname, bool advanced)
<< " -N <int> minimum required neighbors for automatic clustering (default " << DEFAULT_MINPTS << ")" << endl
<< " -S generate and save comparative matrix for clustering" << endl
<< " -L load comparative matrix for clustering" << endl
<< " -C <string> use custom Cost for automatic clustering : format \"match, subst, indels, homo, del_end\" (default "<<Cluster<<" )"<< endl
<< " -C <string> use custom Cost for automatic clustering : format \"match, subst, indels, homo, del_end\" (default "<< DEFAULT_CLUSTER_COST <<" )"<< endl
<< endl ;
cerr << "Detailed output per read (generally not recommended, large files, but may be used for filtering, as in -uu -X 1000)" << endl
......
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