core/segment.cpp, MAX12: KmerSegment a read with the two most frequent KmerAffects

The special germline PSEUDO_GERMLINE_MAX12 uses the usual KmerSegmenter,
but launches computeSegmentation() on the two most frequent KmerAffects of the read.

The 'strand' detection is also more flexible here and purely indicative, as
we could even segment chimera reads.

algo/core/segment.cpp

@@ -26,6 +26,7 @@
 #include "tools.h"
 #include "affectanalyser.h"
 #include <sstream>
+#include <cstring>
 #include <string>
 
 Segmenter::~Segmenter() {}
@@ -196,6 +197,7 @@ KmerSegmenter::KmerSegmenter(Sequence seq, Germline *germline)
   sequence = seq.sequence ;
   info = "" ;
   info_extra = "seed";
+  detected = false ;
   segmented = false;
   segmented_germline = germline ;
   reversed = false;
@@ -233,6 +235,26 @@ KmerSegmenter::KmerSegmenter(Sequence seq, Germline *germline)
 
   KmerAffect before, after;
 
+  if (!strcmp(germline->code.c_str(), PSEUDO_GERMLINE_MAX12))
+    { // Pseudo-germline, max12
+
+      set<KmerAffect> forbidden;
+      forbidden.insert(KmerAffect::getAmbiguous());
+      forbidden.insert(KmerAffect::getUnknown());
+
+      CountKmerAffectAnalyser ckaa(*(germline->index), sequence);
+      pair <KmerAffect, KmerAffect> max12 = ckaa.max12(forbidden);
+
+      strand = nb_strand[0] > nb_strand[1] ? -1 : 1 ;
+      computeSegmentation(strand, max12.first, max12.second);
+
+      // The pseudo-germline should never take precedence over the regular germlines
+      score = 1 ;
+    }
+
+  else
+    { // Regular germline
+
   // Test on which strand we are, select the before and after KmerAffects
   if (nb_strand[0] == 0 && nb_strand[1] == 0) {
     because = UNSEG_TOO_FEW_ZERO ;
@@ -252,9 +274,11 @@ KmerSegmenter::KmerSegmenter(Sequence seq, Germline *germline)
     return ;
   }
 
-  detected = false ;
   computeSegmentation(strand, before, after);
 
+    } // endif Pseudo-germline
+
+
   if (! because)
     {
       // Now we check the delta between Vend and right