core/kmerstore.h, core/segment.cpp: move getProbabilityAtLeastOrAbove to IKmerStore

algo/core/kmerstore.h

@@ -6,6 +6,7 @@
 #include <list>
 #include <stdexcept>
 #include <stdint.h>
+#include <math.h>
 #include "fasta.h"
 #include "tools.h"
 
@@ -84,6 +85,11 @@ public:
    */
   float getIndexLoad() const;
 
+  /**
+   * @return probability that the number of kmers is 'at_least' or more in a sequence of length 'length'
+   */
+  double getProbabilityAtLeastOrAbove(int at_least, int length) const;
+
   /**
    * @return the value of k
    */
@@ -235,6 +241,28 @@ float IKmerStore<T>::getIndexLoad() const {
   return nb_kmers_inserted*1. / (1 << (2 * k));
 }
 
+
+template<class T>
+double IKmerStore<T>::getProbabilityAtLeastOrAbove(int at_least, int length) const {
+
+  // n: number of kmers in the sequence
+  int n = length - getS() + 1;
+  float index_load = getIndexLoad() ;
+
+  double proba = 0;
+  double probability_having_system = pow(index_load, at_least);
+  double probability_not_having_system = pow(1 - index_load, n - at_least);
+  for (int i=at_least; i<=n; i++) {
+    proba += nChoosek(n, i) * probability_having_system * probability_not_having_system;
+    probability_having_system *= index_load;
+    probability_not_having_system /= (1 - index_load);
+  }
+
+  return proba;
+}
+
+
+
 template<class T>
 int IKmerStore<T>::getK() const {
   return k;

algo/core/segment.cpp

@@ -27,7 +27,6 @@
 #include "affectanalyser.h"
 #include <sstream>
 #include <string>
-#include <math.h>
 
 Segmenter::~Segmenter() {}
 
@@ -366,20 +365,8 @@ KmerMultiSegmenter::KmerMultiSegmenter(Sequence seq, MultiGermline *multigermlin
 
 double KmerSegmenter::getProbabilityAtLeastOrAbove(int at_least) const {
 
-  // n: number of kmers in the sequence
-  int n = getSequence().sequence.size() - getKmerAffectAnalyser()->getIndex().getS() + 1;
-  float index_load = getKmerAffectAnalyser()->getIndex().getIndexLoad() ;
-
-  double proba = 0;
-  double probability_having_system = pow(index_load, at_least);
-  double probability_not_having_system = pow(1 - index_load, n - at_least);
-  for (int i=at_least; i<=n; i++) {
-    proba += nChoosek(n, i) * probability_having_system * probability_not_having_system;
-    probability_having_system *= index_load;
-    probability_not_having_system /= (1 - index_load);
-  }
-
-  return proba;
+  return getKmerAffectAnalyser()->getIndex().getProbabilityAtLeastOrAbove(at_least,
+                                                                          getSequence().sequence.size());
 }
 
 double KmerMultiSegmenter::getNbExpected() const {