Commit 00c99d6b authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

vidjil.cpp: -z 0 (max_clones) displays all clones.

It is a very bad idea, we should not let the user use that.
parent 81b11bbd
...@@ -168,7 +168,7 @@ void usage(char *progname) ...@@ -168,7 +168,7 @@ void usage(char *progname)
<< "Limits to report a clone" << endl << "Limits to report a clone" << endl
<< " -R <nb> minimal number of reads supporting a clone (default: " << MIN_READS_CLONE << ")" << 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 << " -% <ratio> minimal percentage of reads supporting a clone (default: " << RATIO_READS_CLONE << ")" << endl
<< " -z <nb> maximal number of clones reported (default: " << MAX_CLONES << ")" << endl << " -z <nb> maximal number of clones reported (0: no limit) (default: " << MAX_CLONES << ")" << endl
<< endl << endl
<< "Fine segmentation options" << endl << "Fine segmentation options" << endl
...@@ -719,7 +719,12 @@ int main (int argc, char **argv) ...@@ -719,7 +719,12 @@ int main (int argc, char **argv)
////////////////////////////////// //////////////////////////////////
//$$ Output clones //$$ Output clones
cout << "Output at most " << max_clones<< " clones with >= " << min_reads_clone << " reads and with a ratio >= " << ratio_reads_clone << endl ; if (max_clones > 0)
cout << "Output at most " << max_clones<< " clones" ;
else
cout << "Output all clones" ;
cout << " with >= " << min_reads_clone << " reads and with a ratio >= " << ratio_reads_clone << endl ;
map <string, int> clones_codes ; map <string, int> clones_codes ;
map <string, string> clones_map_windows ; map <string, string> clones_map_windows ;
...@@ -747,7 +752,7 @@ int main (int argc, char **argv) ...@@ -747,7 +752,7 @@ int main (int argc, char **argv)
++num_clone ; ++num_clone ;
if (num_clone == (max_clones + 1)) if (max_clones && (num_clone == max_clones + 1))
break ; break ;
cout << "#### " ; cout << "#### " ;
......
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