Commit b9e60bce authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

vidjil.cpp: use rather '-e' for e-value

(and use '-E' for old option on forced edges)
parent 05b02185
......@@ -179,7 +179,7 @@ void usage(char *progname, bool advanced)
<< " -m <int> minimal admissible delta between last V and first J k-mer (default: " << DEFAULT_DELTA_MIN << ") (default with -D: " << DEFAULT_DELTA_MIN_D << ")" << endl
<< " -M <int> maximal admissible delta between last V and first J k-mer (default: " << DEFAULT_DELTA_MAX << ") (default with -D: " << DEFAULT_DELTA_MAX_D << ")" << endl
<< " -w <int> w-mer size used for the length of the extracted window (default: " << DEFAULT_W << ") (default with -D: " << DEFAULT_W_D << ")" << endl
<< " -p <float> maximal e-value for determining if a segmentation can be trusted (default: '" << NO_LIMIT << "': no limit)" << endl
<< " -e <float> maximal e-value for determining if a segmentation can be trusted (default: '" << NO_LIMIT << "': no limit)" << endl
<< endl
<< "Window annotations" << endl
......@@ -206,7 +206,7 @@ void usage(char *progname, bool advanced)
<< endl
<< "Additional clustering (experimental)" << endl
<< " -e <file> manual clustering -- a file used to force some specific edges" << endl
<< " -E <file> manual clustering -- a file used to force some specific edges" << endl
<< " -n <int> maximum distance between neighbors for automatic clustering (default " << DEFAULT_EPSILON << "). No automatic clusterisation if =0." << endl
<< " -N <int> minimum required neighbors for automatic clustering (default " << DEFAULT_MINPTS << ")" << endl
<< " -S generate and save comparative matrix for clustering" << endl
......@@ -344,7 +344,7 @@ int main (int argc, char **argv)
//$$ options: getopt
while ((c = getopt(argc, argv, "A!x:X:hHaiI1g:G:V:D:J:k:r:vw:e:C:f:l:c:m:M:N:s:b:Sn:o:L%:y:z:uUK3p:")) != EOF)
while ((c = getopt(argc, argv, "A!x:X:hHaiI1g:G:V:D:J:k:r:vw:e:C:f:l:c:m:M:N:s:b:Sn:o:L%:y:z:uUK3E:")) != EOF)
switch (c)
{
......@@ -461,7 +461,7 @@ int main (int argc, char **argv)
keep_unsegmented_as_clone = true;
break;
case 'p':
case 'e':
expected_value = atof_NO_LIMIT(optarg);
break;
......@@ -522,7 +522,7 @@ int main (int argc, char **argv)
// Clustering
case 'e':
case 'E':
forced_edges = optarg;
break;
......
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