MAJ terminée. Nous sommes passés en version 14.6.2 . Pour consulter les "releases notes" associées c'est ici :

https://about.gitlab.com/releases/2022/01/11/security-release-gitlab-14-6-2-released/
https://about.gitlab.com/releases/2022/01/04/gitlab-14-6-1-released/

Commit e0a39a99 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

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

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