Commit 2bf4496f authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: make the '-r' and '-%' options work with '-c windows'

Runs windowsStorage->keepInterestingWindows even in the case of CMD_WINDOWS.
parent fb472053
......@@ -175,7 +175,7 @@ void usage(char *progname)
<< " -C <string> use custom Cost for automatic clustering : format \"match, subst, indels, homo, del_end\" (default "<<Cluster<<" )"<< endl
<< endl
<< "Limits to report a clone" << endl
<< "Limits to report a clone (or a window)" << endl
<< " -r <nb> minimal number of reads supporting a clone (default: " << MIN_READS_CLONE << ")" << endl
<< " -% <ratio> minimal percentage of reads supporting a clone (default: " << RATIO_READS_CLONE << ")" << endl
<< endl
......@@ -881,7 +881,6 @@ int main (int argc, char **argv)
list< pair <float, int> > norm_list = compute_normalization_list(windowsStorage->getMap(), normalization, nb_segmented);
if (command == CMD_CLONES) {
//////////////////////////////////
//$$ min_reads_clone (ou label)
......@@ -901,6 +900,9 @@ int main (int argc, char **argv)
{
cout << " ! No windows with current parameters." << endl;
}
if (command == CMD_CLONES) {
//////////////////////////////////
//$$ Clustering
......
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