NW now returnes a scaled f32 value

And thereby takes the length of the sequence into account - cleaning
some false positives.

src/fast_mapper/fast_mapper.rs

@@ -764,7 +764,7 @@ impl FastMapper{
             return None
         }
 
-        /*let bad_gene = "Ighm";
+        /*let bad_gene = "Adgrg3";
         let bad = self.get_id( bad_gene.to_string()) ;*/
 
         // check if there is only one gene //

src/fast_mapper/mapper_entries/mapper_entries.rs

@@ -8,7 +8,7 @@ pub struct MapperEntry{
 	pub map:Vec::<(SecondSeq, NameEntry)>, // the data storage
 	only:usize,
 	hamming_cut: u32, // the bit difference up to which a match between two 32bp regions would still be acceptable.
-	needleman_wunsch_cut: u32,
+	needleman_wunsch_cut: f32,
 }
 
 impl MapperEntry{
@@ -22,7 +22,7 @@ impl MapperEntry{
 			map,
 			only :0,
 			hamming_cut :2,
-			needleman_wunsch_cut: 25
+			needleman_wunsch_cut: 0.7
 		}
 	}
 
@@ -99,8 +99,8 @@ impl MapperEntry{
 	/// If this becomes necessary it can be added later.
 	pub fn find (&self, seq:&SecondSeq ) -> Option<Vec<&NameEntry>> {
 		let mut ret : Vec::<&NameEntry> = vec![];
-		let mut dists : Vec::<u32> = vec![];
-		let mut min_dist: u32 = u32::MAX;
+		let mut dists : Vec::<f32> = vec![];
+		let mut min_dist: f32 = f32::MAX;
 		for i in 0..self.map.len() {
 			//eprintln!("Hamming distance below {} - returning {:?}", self.hamming_cut, self.map[i].1.data );
 			//let dist = self.map[i].0.hamming_distance( seq );
@@ -221,4 +221,4 @@ mod tests {
     	assert_eq!(this.map[0].1.data[0], (2_usize, 2_usize));
     }
 
-}
+}

src/fast_mapper/mapper_entries/second_seq.rs

@@ -99,7 +99,7 @@ impl SecondSeq {
 
     /// Almost a needleman_wunsch implementation. It just returns the difference from the expected result
     /// comparing the sequences in there minimal defined length. Similar to the hamming_distance function.
-    pub fn needleman_wunsch(&self, other: &SecondSeq ) -> u32 {
+    pub fn needleman_wunsch(&self, other: &SecondSeq ) -> f32 {
 
         let size = self.min_length(other);
 
@@ -154,7 +154,7 @@ impl SecondSeq {
             println!();
         }*/
 
-        (size as i32 - matrix[rows - 1][cols - 1].score).abs() as u32
+        (size as i32 - matrix[rows - 1][cols - 1].score).abs() as f32 / size as f32
     }
 
     /// returns the minimal size the two SecondSeq obejcts are defined for
@@ -230,7 +230,7 @@ impl SecondSeq {
         println!("{} sig bp", self.1);
     }
 
-    pub fn fuzzy_match(&self, other:&SecondSeq, max_dist:u32 ) -> bool {
+    pub fn fuzzy_match(&self, other:&SecondSeq, max_dist:f32 ) -> bool {
 
         //return self.hamming_distance( other ) <= max_dist.try_into().unwrap()
         return self.needleman_wunsch( other ) <= max_dist.try_into().unwrap()
@@ -340,4 +340,4 @@ mod tests {
         let seq6 = SecondSeq(0b0, 20);
         assert_eq!( seq1.hamming_distance( &seq6 ), 3 );
     }
-}
+}