Commit 14c14fe2 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: option -A, outputs absolutely all clones

This is again a very bad idea. Only for short datasets.
parent 00c99d6b
......@@ -169,6 +169,7 @@ void usage(char *progname)
<< " -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
<< " -z <nb> maximal number of clones reported (0: no limit) (default: " << MAX_CLONES << ")" << endl
<< " -A reports all clones (-r 0 -R 1 -% 0 -z 0), to be used only on very small datasets" << endl
<< endl
<< "Fine segmentation options" << endl
......@@ -264,7 +265,7 @@ int main (int argc, char **argv)
//$$ options: getopt
while ((c = getopt(argc, argv, "haG:V:D:J:k:r:R:vw:e:C:t:l:dc:m:M:N:s:p:Sn:o:Lx%:Z:z:u")) != EOF)
while ((c = getopt(argc, argv, "AhaG:V:D:J:k:r:R:vw:e:C:t:l:dc:m:M:N:s:p:Sn:o:Lx%:Z:z:u")) != EOF)
switch (c)
{
......@@ -357,6 +358,8 @@ int main (int argc, char **argv)
prefix_filename = optarg;
break;
// Limits
case 'r':
min_reads_window = atoi(optarg);
break;
......@@ -372,6 +375,16 @@ int main (int argc, char **argv)
case 'z':
max_clones = atoi(optarg);
break;
case 'A': // --all
min_reads_window = 1 ;
ratio_reads_clone = 0 ;
min_reads_clone = 0 ;
max_clones = 0 ;
break ;
// Seeds
case 's':
#ifndef NO_SPACED_SEEDS
seed = string(optarg);
......
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