diff --git a/src/kmer_similarity.c b/src/kmer_similarity.c
index 74f8e8d..a9787a6 100755
--- a/src/kmer_similarity.c
+++ b/src/kmer_similarity.c
@@ -78,8 +78,7 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
 	Obi_ali_p       ali = NULL;
 	int 			i, j;
 	bool 			switched_seqs;
-	bool			left_ali;
-	double 			score = 0.0;
+	int 			score = 0;
 	Obi_blob_p      blob1 = NULL;
 	Obi_blob_p   	blob2 = NULL;
 	Obi_blob_p   	temp_blob = NULL;
@@ -397,8 +396,6 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
 			keep_seq2_end = true;
 	}
 
-	score = max_common_kmers + kmer_size - 1;
-
 	ali = (Obi_ali_p) malloc(sizeof(Obi_ali_t));
 	if (ali == NULL)
 	{
@@ -407,6 +404,7 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
 	 	return NULL;
 	}
 
+	score = max_common_kmers + kmer_size - 1;  // aka the number of nucleotides in the longest stretch of kmers perfectly matching
 	abs_shift = abs(best_shift);
 
 	// Save result in Obi_ali structure
@@ -417,15 +415,9 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
 	ali->consensus_seq = NULL;
 	ali->consensus_qual = NULL;
 	if (((best_shift <= 0) && (!switched_seqs)) || ((best_shift > 0) && switched_seqs))
-	{
-		left_ali = true;
 		strcpy(ali->direction, "left");
-	}
 	else
-	{
-		left_ali = false;
 		strcpy(ali->direction, "right");
-	}
 
 	// Build the consensus sequence if asked
 	if (build_consensus)
diff --git a/src/kmer_similarity.h b/src/kmer_similarity.h
index 2d2b920..738fccf 100755
--- a/src/kmer_similarity.h
+++ b/src/kmer_similarity.h
@@ -27,7 +27,7 @@
  * @brief Alignment structure, with informations about the similarity and to rebuild the alignment.
  */
 typedef struct Obi_ali {
-	double   score;	    		/**< Alignment score.
+	int      score;	    		/**< Alignment score, corresponding to the number of matches (identical nucleotides aligned).
 	 	 	 	 	 	 	 	 */
 	int      consensus_length; 	/**< Length of the final consensus sequence.
 	 	 	 	 	 	 	 	 */
@@ -37,10 +37,10 @@ typedef struct Obi_ali {
 	 	 	 	 	 	 	 	 */
 	uint8_t* consensus_qual;	/**< Consensus quality built as to reconstruct a pairedend read.
 	 	 	 	        	 	 */
-	int		 shift;   		    /**< Shift chosen to align the sequences (for shifted alignment).
+	int		 shift;   		    /**< Shift chosen to align the sequences.
 	 	 	 	 	 	 	 	 */
-	char     direction[6]; 	    /**< Alignement direction (positive/right or negative/left shift) (for shifted alignment).
-	 	 	 	 	 	 	 	 */   // TODO but sequences switched around depending on size..... discuss
+	char     direction[6]; 	    /**< Alignment direction (positive/right or negative/left shift).
+								 */
 } Obi_ali_t, *Obi_ali_p;