algo/core/{kmerstore.h,germline.cpp,affectanalyser.cpp}: Hack for the xxx germline

See #2596 for the reason why we need to do this.
This should be reverted with #1169

algo/core/affectanalyser.cpp

@@ -217,10 +217,16 @@ affect_infos KmerAffectAnalyser::getMaximum(const KmerAffect &before,
       results.nb_before_right++;
   }
 
-  left_evalue = kms.getProbabilityAtLeastOrAbove(before,
+  KmerAffect left_affect = before;
+  KmerAffect right_affect = after;
+  if (kms.multiple_in_one) {
+    left_affect = AFFECT_NOT_UNKNOWN;
+    right_affect = AFFECT_NOT_UNKNOWN;
+  }
+  left_evalue = kms.getProbabilityAtLeastOrAbove(left_affect,
                                                  results.nb_before_left,
                                                  1 + results.last_pos_max);
-  right_evalue = kms.getProbabilityAtLeastOrAbove(after,
+  right_evalue = kms.getProbabilityAtLeastOrAbove(right_affect,
                                                   results.nb_after_right,
                                                   seq.size() - 1 - results.first_pos_max);
 
@@ -244,7 +250,11 @@ affect_infos KmerAffectAnalyser::getMaximum(const KmerAffect &before,
 
 
 double KmerAffectAnalyser::getProbabilityAtLeastOrAbove(const KmerAffect &kmer, int at_least) const {
-  return kms.getProbabilityAtLeastOrAbove(kmer, at_least, seq.size());
+  KmerAffect affect = kmer;
+  if (kms.multiple_in_one) {
+    affect = AFFECT_NOT_UNKNOWN;
+  }
+  return kms.getProbabilityAtLeastOrAbove(affect, at_least, seq.size());
 }
 
 pair <double, double> KmerAffectAnalyser::getLeftRightProbabilityAtLeastOrAbove() const {

algo/core/germline.cpp

@@ -387,6 +387,7 @@ void MultiGermline::build_with_one_index(string seed, bool set_index)
   index = KmerStoreFactory<KmerAffect>::createIndex(indexType, expand_seed(seed), rc);
   index->refs = 1;
   insert_in_one_index(index, set_index);
+  index->multiple_in_one = true;
 }
 
 void MultiGermline::finish() {

algo/core/kmerstore.h

@@ -82,6 +82,7 @@ public:
   static int last_id;
   int id; // id of this index
   int refs; // number of germlines using this index
+  bool multiple_in_one;
 
   list< pair <T, BioReader> > labels;
 
@@ -205,6 +206,7 @@ IKmerStore<T>::IKmerStore() {
   id = ++last_id;
   refs = 0;
   finished_building = false;
+  multiple_in_one = false;
 }
 
 template<class T> int IKmerStore<T>::last_id = 0;