Commit e0a39a99 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: no limit value for '-y' and '-z' options is given by the 'all' keyword

parent e38b9ab5
......@@ -75,6 +75,7 @@
#define DEFAULT_MAX_REPRESENTATIVES 100
#define MAX_CLONES 20
#define RATIO_READS_CLONE 0.0
#define NO_LIMIT "all"
#define COMMAND_WINDOWS "windows"
#define COMMAND_CLONES "clones"
......@@ -183,9 +184,9 @@ void usage(char *progname)
<< endl
<< "Limits to further analyze some clones" << endl
<< " -y <nb> maximal number of clones computed with a representative (-1: no limit) (default: " << DEFAULT_MAX_REPRESENTATIVES << ")" << endl
<< " -z <nb> maximal number of clones to be segmented (-1: no limit, do not use) (default: " << MAX_CLONES << ")" << endl
<< " -A reports and segments all clones (-r 0 -% 0 -y -1 -z -1), to be used only on very small datasets" << endl
<< " -y <nb> maximal number of clones computed with a representative ('" << NO_LIMIT << "': no limit) (default: " << DEFAULT_MAX_REPRESENTATIVES << ")" << endl
<< " -z <nb> maximal number of clones to be segmented ('" << NO_LIMIT << "': no limit, do not use) (default: " << MAX_CLONES << ")" << endl
<< " -A reports and segments all clones (-r 0 -% 0 -y " << NO_LIMIT << " -z " << NO_LIMIT << "), to be used only on very small datasets" << endl
<< endl
<< "Fine segmentation options (second pass, see warning in doc/algo.org)" << endl
......@@ -408,10 +409,20 @@ int main (int argc, char **argv)
break;
case 'y':
if (!strcmp(NO_LIMIT, optarg))
{
max_representatives = -1;
break;
}
max_representatives = atoi(optarg);
break;
case 'z':
if (!strcmp(NO_LIMIT, optarg))
{
max_clones = -1;
break;
}
max_clones = atoi(optarg);
break;
......
......@@ -110,9 +110,9 @@ Limits to report a clone (or a window)
-% <ratio> minimal percentage of reads supporting a clone (default: 0)
Limits to further analyze some clones
-y <nb> maximal number of clones computed with a representative (0: no limit) (default: 100)
-z <nb> maximal number of clones to be segmented (0: no limit, do not use) (default: 20)
-A reports and segments all clones (-r 0 -% 0 -z 0), to be used only on very small datasets
-y <nb> maximal number of clones computed with a representative ('all': no limit) (default: 100)
-z <nb> maximal number of clones to be segmented ('all': no limit, do not use) (default: 20)
-A reports and segments all clones (-r 1 -% 0 -y all -z all), to be used only on very small datasets
#+END_EXAMPLE
The =-r/-%= options are strong thresholds: if a clone does not have
......@@ -125,7 +125,7 @@ MRD detection).
The =-y= option limits the number of clones for which a representative
sequence is computed. Usually you do not need to have more
representatives (see below), but you can safely put =-y 0= if you want
representatives (see below), but you can safely put =-y all= if you want
to compute all representative sequences.
The =-z= option limits the number of clones that are fully analyzed,
......
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