Commit 214fd38b authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

vidjil.cpp: warn if there are some clones without representative sequence

parent f88ee197
......@@ -775,6 +775,7 @@ int main (int argc, char **argv)
VirtualReadScore *scorer = new KmerAffectReadScore(*index);
int num_clone = 0 ;
int clones_without_representative = 0 ;
ofstream out_edges((out_dir+prefix_filename + EDGES_FILENAME).c_str());
int nb_edges = 0 ;
......@@ -886,8 +887,16 @@ int main (int argc, char **argv)
ratio_representative,
max_auditionned);
if (representative == NULL_SEQUENCE) {
clones_without_representative++ ;
if (verbose)
cout << "# (no representative sequence with current parameters)" ;
} else {
//$$ There is one representative, FineSegmenter
if (representative != NULL_SEQUENCE) {
representative.label = string_of_int(it->second) + "-"
+ representative.label;
FineSegmenter seg(representative, rep_V, rep_J, delta_min, delta_max, segment_cost);
......@@ -1147,12 +1156,20 @@ int main (int argc, char **argv)
SimilarityMatrix matrix = compare_all(representatives_this_clone, true);
cout << RawOutputSimilarityMatrix(matrix, 90);
}
//$$ End of very_detailed_cluster_analysis
out_edges.close() ;
cout << "#### end of clones" << endl;
cout << endl;
if (clones_without_representative > 0)
{
cout << clones_without_representative << " clones without representatives" ;
cout << " (requiring " << min_cover_representative << "/" << ratio_representative << " supporting reads)" << endl ;
cout << endl ;
}
//$$ Compare representatives of all clones
if (detailed_cluster_analysis)
......
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