kmerstore.h: Insert properly the revcomp kmers with unsymmetrical seeds.

If the seed is not symmetrical (as with TRA and VdJa), we can't just reverse the seed.
We need to take back the original substring, reverse it and then take the seed.

algo/core/kmerstore.h

@@ -208,7 +208,8 @@ void IKmerStore<T>::insert(const seqtype &sequence,
                            const string &label,
                            bool ignore_extended_nucleotides){
   for(size_t i = 0 ; i + s < sequence.length() + 1 ; i++) {
-    seqtype kmer = spaced(sequence.substr(i, s), seed);
+    seqtype substr = sequence.substr(i, s);
+    seqtype kmer = spaced(substr, seed);
 
     if (ignore_extended_nucleotides && has_extended_nucleotides(kmer))
       continue;
@@ -227,7 +228,7 @@ void IKmerStore<T>::insert(const seqtype &sequence,
     }
     this_kmer += T(label, strand);
     if (revcomp_indexed && ! T::hasRevcompSymetry()) {
-      seqtype rc_kmer = revcomp(kmer);
+      seqtype rc_kmer = spaced(revcomp(substr), seed);
       T &this_rc_kmer = this->get(rc_kmer);
       if (this_rc_kmer.isNull())
         nb_kmers_inserted++;

algo/tests/vidjil_revcomp_VdJa.should_get

 !LAUNCH: ../../vidjil -i -g ../../germline/ -r 1 -c clones ../../data/revcomp-VdJa.fa
 
 $ Just one window found
-f1:==> found 1 ..-windows
+1:==> found 1 ..-windows
 
 $ Just one clone found
-f1:==> 1 clones
+1:==> 1 clones
 
 $ Two reads segmented in VdJa
 1:VdJa -> 2
 
 $ segmentation for the main clone
-f1:TRDV1.01 5//3 TRDD2.01 1//7 TRAJ29
+1:TRDV1.01 5//3 TRDD2.01 1//7 TRAJ29