Commit 606b9bef authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: -w all

See #1642.
parent abff4ef3
......@@ -194,7 +194,7 @@ void usage(char *progname, bool advanced)
#ifndef NO_SPACED_SEEDS
<< " (using -k option is equivalent to set with -s a contiguous seed with only '#' characters)" << endl
#endif
<< " -w <int> w-mer size used for the length of the extracted window (default: " << DEFAULT_W << ")" << endl
<< " -w <int> w-mer size used for the length of the extracted window (default: " << DEFAULT_W << ") ('" << NO_LIMIT << "': use all the read, no window clustering)" << endl
<< " -e <float> maximal e-value for determining if a V-J segmentation can be trusted (default: " << THRESHOLD_NB_EXPECTED << ")" << endl
<< " -t <int> trim V and J genes (resp. 5' and 3' regions) to keep at most <int> nt (default: " << DEFAULT_TRIM << ") (0: no trim)" << endl
<< endl
......@@ -512,7 +512,7 @@ int main (int argc, char **argv)
break;
case 'w':
wmer_size = atoi(optarg);
wmer_size = atoi_NO_LIMIT(optarg);
break;
case 'm':
......@@ -721,7 +721,7 @@ int main (int argc, char **argv)
#endif
if (wmer_size < 0)
if ((wmer_size< 0) && (wmer_size!= NO_LIMIT_VALUE))
{
cerr << ERROR_STRING << "Too small -w. The window size should be positive" << endl;
exit(1);
......@@ -1120,8 +1120,12 @@ int main (int argc, char **argv)
int nb_segmented = we.getNbSegmented(TOTAL_SEG_AND_WINDOW);
float ratio_segmented = 100 * (float) nb_segmented / nb_total_reads ;
stream_segmentation_info << " ==> found " << windowsStorage->size() << " " << wmer_size << "-windows"
<< " in " << nb_segmented << " reads"
if (wmer_size != NO_LIMIT_VALUE)
stream_segmentation_info << " ==> found " << windowsStorage->size() << " " << wmer_size<< "-windows in " ;
else
stream_segmentation_info << " ==> consider as windows these " ;
stream_segmentation_info << nb_segmented << " reads"
<< " (" << setprecision(3) << ratio_segmented << "% of " << nb_total_reads << " reads)" << endl ;
// warn if there are too few segmented sequences
......
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