core/segment.cpp: UNSEG_ONLY_V/J only when left/right e-values are good enough

There were previously two places where the segmentation could fail with UNSEG_ONLY_V/J.
The first one, when there is no 'good' segmentation point, was improved by 5298c86f, requiring at least 5 k-mers.
It turned out that it was not sufficient, as reported by @flothoni in #2107.

Contrarily to what what thought in 5298c86f, the segmentation point returned by kaa->getMaximum()
is actually meaningful to compute some e-values, even when kaa->getMaximum().max_found is false.

We thus now remove completely some ancient code where the thresholds were based on the number of k-mers,
and rely solely on checkLeftRightEvaluesThreshold() to discriminate between these unsegmentation causes.

Streamlines the code, and will fix #2107.

algo/core/segment.cpp

@@ -612,36 +612,25 @@ void KmerSegmenter::computeSegmentation(int strand, KmerAffect before, KmerAffec
   affect_infos max;
   max = kaa->getMaximum(before, after);
 
-  // We did not find a good segmentation point
-  if (!max.max_found) {
-    // We labeled it detected if there were both enough affect_5 and enough affect_3
-    bool detected_before = (max.nb_before_left + max.nb_before_right >= DETECT_THRESHOLD);
-    bool detected_after = (max.nb_after_left + max.nb_after_right >= DETECT_THRESHOLD);
-
-    if (detected_before && detected_after)
-      because = UNSEG_AMBIGUOUS ;
-    else if ((strand == 1 && detected_before) || (strand == -1 && detected_after))
-      because = UNSEG_TOO_FEW_J ;
-    else if ((strand == 1 && detected_after) || (strand == -1 && detected_before))
-      because = UNSEG_TOO_FEW_V ;
-    else
-      because = UNSEG_TOO_FEW_ZERO ;
-
-    return ;
-  }
-
-
   // E-values
   pair <double, double> pvalues = kaa->getLeftRightProbabilityAtLeastOrAbove();
   evalue_left = pvalues.first * multiplier ;
   evalue_right = pvalues.second * multiplier ;
   evalue = evalue_left + evalue_right ;
 
+  // This can lead to UNSEG_TOO_FEW_ZERO or UNSEG_TOO_FEW_V/J
   checkLeftRightEvaluesThreshold(threshold, strand);
 
   if (because != NOT_PROCESSED)
     return ;
 
+  if (!max.max_found) {
+    // The 'ratioMin' checks at the end of kaa->getMaximum() failed
+    because = UNSEG_AMBIGUOUS;
+    return ;
+  }
+  
+
    // There was a good segmentation point
 
    box_V->end = max.first_pos_max;

algo/core/segment.h

@@ -23,13 +23,7 @@
 
 #define DETECT_THRESHOLD_STRAND 5   /* If the number of total affectations
                                        is above this threshold, then a sequence with no clearly attributed
-                                       stranf will be marked as STRAND_NOT_CONSISTEN */
-
-#define DETECT_THRESHOLD 5      /* This threshold only affects the classification of unsegmented sequences.
-                                   If the numbers of both V and J affectations are above this threshold,
-                                   then the unsegmented sequence will be marked as AMBIGUOUS.
-                                   Otherwise, if the number of either V or J affectations if above this threshold,
-                                   then the unsegmented sequence will be marked as either ONLY V or ONLY J. */
+                                       strand will be marked as STRAND_NOT_CONSISTENT */
 
 #define JSON_REMEMBER_BEST  4   /* The number of V/D/J predictions to keep  */