read_score.{h,cpp} representative.cpp: Define a random score on a read and use it

Random score on a read makes possible to have a random sample of reads to compute the representative.
Thus the representative will be built on a really representative sample.

Our attempts to have a good quality sample have failed so far. Thus we attempt this solution.

Fix #3764

algo/core/read_score.cpp

@@ -101,3 +101,15 @@ float ReadQualityScore::getScore(const Sequence &sequence) const {
     percent_quality = GOOD_QUALITY;
   return percent_quality * sequence.sequence.size() / GOOD_QUALITY;
 }
+
+////////////////////////////////////////////////////////////////////////////////
+//////////////////////////////  RandomScore  ///////////////////////////////
+////////////////////////////////////////////////////////////////////////////////
+
+RandomScore::RandomScore(){srand(1);} // Ensures a deterministic output
+RandomScore::~RandomScore(){}
+
+float RandomScore::getScore(const Sequence &sequence) const {
+  UNUSED(sequence);
+  return rand() % 500;
+}

algo/core/read_score.h

@@ -91,4 +91,17 @@ class ReadQualityScore: public VirtualReadScore {
    */
   float getScore(const Sequence &sequence) const;
 };
+
+/**
+ * A very simple implementation of VirtualReadScore.
+ * The score is random.
+ */
+class RandomScore: public VirtualReadScore {
+ public:
+  RandomScore();
+  ~RandomScore();
+
+  float getScore(const Sequence &sequence) const;
+};
+
 #endif

algo/core/representative.cpp

@@ -114,8 +114,8 @@ void KmerRepresentativeComputer::compute(bool try_hard) {
       index[i]->insert(it->sequence, it->label, false, 0, seeds[i]);
   }
 
-  // Create a read chooser to have the sequences sorted by length
-  ReadQualityScore *rlc = new ReadQualityScore();
+  // Create a read chooser to have the sequences sorted on the criteria we want
+  VirtualReadScore *rlc = new RandomScore();
   ReadChooser rc(sequences, *rlc);
   delete rlc;