Commit 05b02185 authored by Mathieu Giraud's avatar Mathieu Giraud

segment.{h,cpp}, vidjil.cpp: by default, skips the E-value check ('all' argument)

parent 90a27598
......@@ -347,6 +347,8 @@ KmerMultiSegmenter::KmerMultiSegmenter(Sequence seq, MultiGermline *multigermlin
delete kseg;
}
} // end for (Germlines)
if (threshold_nb_expected > NO_LIMIT_VALUE)
if (the_kseg->isSegmented() && getNbExpected() > threshold_nb_expected)
the_kseg->setSegmentationStatus(UNSEG_NOISY);
}
......
......@@ -28,7 +28,11 @@
#define JSON_REMEMBER_BEST 4 /* The number of V/D/J predictions to keep */
#define THRESHOLD_NB_EXPECTED 100 /* Threshold of the accepted expected value for number of found k-mers */
#define NO_LIMIT_VALUE -1
#define THRESHOLD_NB_EXPECTED NO_LIMIT_VALUE /* Threshold of the accepted expected value for number of found k-mers */
using namespace std;
......
......@@ -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: " << THRESHOLD_NB_EXPECTED <<")" << endl
<< " -p <float> maximal e-value for determining if a segmentation can be trusted (default: '" << NO_LIMIT << "': no limit)" << endl
<< endl
<< "Window annotations" << endl
......@@ -247,7 +247,11 @@ void usage(char *progname, bool advanced)
int atoi_NO_LIMIT(char *optarg)
{
return strcmp(NO_LIMIT, optarg) ? atoi(optarg) : -1 ;
return strcmp(NO_LIMIT, optarg) ? atoi(optarg) : NO_LIMIT_VALUE ;
}
int atof_NO_LIMIT(char *optarg)
{
return strcmp(NO_LIMIT, optarg) ? atof(optarg) : NO_LIMIT_VALUE ;
}
int main (int argc, char **argv)
......@@ -458,7 +462,7 @@ int main (int argc, char **argv)
break;
case 'p':
expected_value = atof(optarg);
expected_value = atof_NO_LIMIT(optarg);
break;
// Output
......
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