Commit 13a66d7d authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: '-F' option sets only_labeled_windows

parent 03abd35c
......@@ -184,6 +184,7 @@ void usage(char *progname, bool advanced)
<< "Window annotations" << endl
<< " -l <file> labels for some windows -- these windows will be kept even if -r/-% thresholds are not reached" << endl
<< " -F filter -- keep only the labeled windows" << endl
<< endl ;
cerr << "Limits to report a clone (or a window)" << endl
......@@ -345,7 +346,7 @@ int main (int argc, char **argv)
//$$ options: getopt
while ((c = getopt(argc, argv, "A!x:X:hHaiI12g:G:V:D:J:k:r:vw:e:C:f:l:c:m:M:N:s:b:Sn:o:L%:y:z:uUK3E:")) != EOF)
while ((c = getopt(argc, argv, "A!x:X:hHaiI12g:G:V:D:J:k:r:vw:e:C:f:l:Fc:m:M:N:s:b:Sn:o:L%:y:z:uUK3E:")) != EOF)
switch (c)
{
......@@ -523,6 +524,10 @@ int main (int argc, char **argv)
windows_labels_file = optarg;
break;
case 'F':
only_labeled_windows = true;
break;
// Clustering
case 'E':
......@@ -1022,8 +1027,17 @@ int main (int argc, char **argv)
//$$ min_reads_clone (ou label)
int min_reads_clone_ratio = (int) (ratio_reads_clone * nb_segmented / 100.0);
cout << "Considering only labeled windows and windows with >= " << min_reads_clone << " reads"
<< " and with a ratio >= " << ratio_reads_clone << " (" << min_reads_clone_ratio << ")" << endl ;
cout << "Considering ";
if (only_labeled_windows)
cout << "only labeled windows" ;
if (!only_labeled_windows)
cout << "labeled windows"
<< " and windows with >= " << min_reads_clone << " reads"
<< " and with a ratio >= " << ratio_reads_clone << " (" << min_reads_clone_ratio << ")" ;
cout << endl ;
int min_reads_clone_final = max(min_reads_clone, min_reads_clone_ratio);
......
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