Merge branch 'feature-a/3414-output-equal-score-alternative-genes' into 'dev'

Algo: output equal score alternative genes

Closes #3414

See merge request !459

algo/core/segment.cpp

@@ -91,11 +91,14 @@ void AlignBox::addToOutput(CloneOutput *clone, int alternative_genes) {
   clone->setSeg(key, j) ;
 
   /*Export the N best genes if threshold parameter is specified*/
-  if(rep && !this->score.empty() && rep->size() <= (int)this->score.size() && alternative_genes > 0 && alternative_genes <= (int)this->score.size()){
+  if(rep && !this->score.empty() && rep->size() <= (int)this->score.size() && alternative_genes > 0){
     json jalt = json::array();
-    for(int i = 0; i < alternative_genes;++i){
+    int last_score = this->score[0].first;
+    for(int i = 0; i < (int)this->score.size() &&
+          (i < alternative_genes || last_score == this->score[i].first);++i){
       int r = this->score[i].second;
       jalt.push_back(json::object({{"name",rep->label(r)}}));
+      last_score = this->score[i].first;
     }
     clone->setSeg(key + "alt", jalt);
   }

algo/core/segment.h

@@ -135,7 +135,7 @@ class AlignBox
   /* Marked position, for Cys104 and Phe118/Trp118 */
   int marked_pos;
 
-  /* Identifiers and scores of other possible reference sequence */
+  /* Scores and identifiers of other possible reference sequence */
   vector<pair<int, int> > score;
 };
 

algo/tests/should-get-tests/alternative_genes.should-get

@@ -5,7 +5,9 @@ $ Presence of alternative:
 1: "3alt"
 1: "name": "IGHJ4.02"
 1: "name": "IGHJ4.01"
-1a: "name": "IGHJ5.01"
+1: "name": "IGHJ5.01"
+1: "name": "IGHJ5.02"
+0: "name": "IGHJ[1236]
 1: "4alt"
 1: "name": "IGHD3-22.01"
 1: "name": "IGHD3-10.02"
@@ -15,5 +17,5 @@ $ Presence of alternative:
 1: "name": "IGHV3-48.02"
 1: "name": "IGHV3-48.04"
 
-$ Correct number of "name" fields (1 clone + 3*1 'best' genes + 3*3 'alternative' genes)
-w13:"name"
+$ Correct number of "name" fields (1 clone + 3*1 'best' genes + 2*3 'alternative' genes + 4 alternative J genes)
+w14:"name"