alignpairedend: improved/fixed the output tags for the alignment score

and lengths. Removed minimum score option

src/kmer_similarity.c

@@ -414,7 +414,10 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
 	}
 
 	if (max_common_kmers > 0)
-		score = max_common_kmers + kmer_size - 1;  // aka the number of nucleotides in the longest stretch of kmers perfectly matching
+		score = max_common_kmers + kmer_size - 1; // aka an approximation of the number of nucleotides matching in the overlap of the alignment.
+												  // It's an approximation because one mismatch produces kmer_size kmer mismatches if in the middle of the overlap,
+												  // and less for mismatches located towards the ends of the overlap. The case where there are the most mismatches is assumed,
+												  // meaning that the score will be often underestimated and never overestimated.
 	else
 		score = 0;
 	abs_shift = abs(best_shift);