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

algo/core/segment.cpp

@@ -347,8 +347,10 @@ KmerMultiSegmenter::KmerMultiSegmenter(Sequence seq, MultiGermline *multigermlin
         delete kseg;
       }
     } // end for (Germlines)
-  if (the_kseg->isSegmented() && getNbExpected() > threshold_nb_expected)
-    the_kseg->setSegmentationStatus(UNSEG_NOISY);
+
+  if (threshold_nb_expected > NO_LIMIT_VALUE)
+    if (the_kseg->isSegmented() && getNbExpected() > threshold_nb_expected)
+      the_kseg->setSegmentationStatus(UNSEG_NOISY);
 }
 
 double KmerSegmenter::getProbabilityAtLeastOrAbove(int at_least) const {

algo/core/segment.h

@@ -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;
 

algo/vidjil.cpp

@@ -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