No Idea what I changed here.

src/analysis/gene_mapper.rs

@@ -40,7 +40,7 @@ use std::thread;
 use rayon::prelude::*;
 use rayon::slice::ParallelSlice;
 
-use crate::ofiles::{Ofiles, Fspot};
+use crate::ofiles::{Ofiles};
 //use std::fs::write;
 
 //static EMPTY_VEC: Vec<String> = Vec::new();

src/analysis/genomic_mapper.rs

@@ -44,7 +44,7 @@ use std::thread;
 use rayon::prelude::*;
 use rayon::slice::ParallelSlice;
 
-use crate::ofiles::{Ofiles, Fspot};
+use crate::ofiles::{Ofiles};
 //use std::fs::write;
 use glob::glob;
 

src/gene.rs

@@ -76,14 +76,12 @@ impl Gene{
 			Err(e) => panic!("I could not parse the end of the transcript as usize: {e:?}"),
 		};
 
-		let sense_strand = sense_strand_s == "+";
-
 		Self{
 			chrom: chrom.to_string(),
 			start,
 			end,
 			exons,
-			sense_strand,
+			sense_strand: match sense_strand_s{ "+" => true, _ => false },
 			name: name.to_string(),
 			transcript: transcript.to_string(),
 			ids,
@@ -165,10 +163,10 @@ impl Gene{
 
 	/// generate mRNA and nacent RNA (if the last exon is small enough)
 	pub fn generate_rna_and_nascent_strings(&self, seq: &[u8], covered_area: usize) -> (Option<Vec<u8>>, Option<Vec<u8>>) {
-	    let mrna = self.to_mrna(seq.to_owned(), covered_area);
+	    let nascent = self.to_nascent( seq, covered_area );
+	    let mrna = self.to_mrna( seq, covered_area );
 
-	    let nascent = self.to_nascent(seq.to_owned(), covered_area);
-	    (mrna, nascent)
+	    ( mrna, nascent)
 	}
 
 	/// returns the start position on the mRNA in genomic coordinates and the global end position
@@ -196,7 +194,7 @@ impl Gene{
 	/// get the mRNA sequence of the transcript in sense orientation.
 	/// Fails if any other base than AGCT is in the sequence
 	/// This returns the revers complement if on the opposite starnd
-	pub fn to_mrna(&self, seq: Vec<u8>, covered_area:usize) -> Option<Vec<u8>> {
+	pub fn to_mrna(&self, seq: &[u8], covered_area:usize) -> Option<Vec<u8>> {
 
 	    let mut mrna = Vec::<u8>::with_capacity(seq.len() ); // Allocate more space for potential additions
 
@@ -216,12 +214,12 @@ impl Gene{
 			mrna.extend_from_slice(&seq[reg[0] - 1..(reg[1])]);
 	    }
 	    //println!("the final mRNA   {:?}", std::str::from_utf8(&mrna) );
-	    self.cut_to_size(mrna, covered_area )
+	    self.cut_to_size( &mrna, covered_area )
 
 	}
 
 	/// cut the RNA to the right size
-	fn cut_to_size( &self, seq:Vec<u8>, covered_area:usize) -> Option<Vec<u8>> {
+	fn cut_to_size( &self, seq: &[u8], covered_area:usize) -> Option<Vec<u8>> {
 
 		let start = seq.len().saturating_sub(covered_area);
 		if ! self.sense_strand{
@@ -244,7 +242,7 @@ impl Gene{
 	/// get the nascent RNA for this transcript (including introns).
 	/// Fails if any other base than AGCT is in the sequence
 	/// This returns the revers complement if on the opposite starnd
-	fn to_nascent(&self, seq:Vec<u8> , covered_area:usize) -> Option<Vec<u8>> {
+	fn to_nascent(&self, seq: &[u8] , covered_area:usize) -> Option<Vec<u8>> {
 		if self.exons.len() == 0{
 			eprintln!("I have no exons?! - something is wrong here! {self}");
 			return None
@@ -266,15 +264,15 @@ impl Gene{
 			let (_glob_start, _glob_end) = self.to_mrna_positions(covered_area);
 			//make the nascent WAY longer??
 			//self.cut_to_size(nascent, glob_end - glob_start )
-			self.cut_to_size(nascent, covered_area*2 )
+			self.cut_to_size(&nascent, covered_area*2 )
 		}
 		else {
 			None
 		}
 	}
 
 	/// the reverse complement of a Vec<u8>
-    fn rev_compl( seq:Vec<u8> ) -> Vec<u8>{
+    fn rev_compl( seq:&[u8] ) -> Vec<u8>{
 	    seq.iter()
 	        .rev()
 	        .filter_map(|&c| COMPLEMENT[c as usize])

src/genes_mapper/genes_mapper.rs

@@ -416,67 +416,6 @@ impl GenesMapper{
         //println!("\nMakes sense? {:?}", data);
         data
     }
-
-    /*fn query_database( &self, seq: &[u8] ) -> Vec<((usize, i32), usize)> {
-    	//if self.small_entries {
-    		return self.query_database_small( seq );
-    	//}
-		let mut res = HashMap::<(usize, i32), usize>::new();// Vec<i32>>::new();
-		let mut read_data = GeneData::new( seq,"read_t", "read", "read2", 0 );
-		let mut i = 0;
-		let mut failed = 0;
-
-		while let Some((key, start)) = read_data.next(){
-
-			//println!("after {i} (matching) iterations ({}) the res looks like that {res:?}", Self::key_to_string( &key) );
-			if self.reject_key(&key){
-				continue;
-			}
-			
-			if ! self.mapper[key as usize].is_empty() {
-				i+=1;
-				failed = 0;
-				#[cfg(debug_assertions)]
-				if self.debug {
-					let values: Vec<_> = self.mapper[key as usize].data().collect();
-					let m = 9.min( values.len() );
-					println!("I am testing this key: {} and got {:?} ...", Self::as_dna_string(&key) , &values[0..m] );
-				}
-				// this will directly modify the res HashMap as it can also find more than one!
-				self.mapper[key as usize].get( &mut res, start as i32 );
-			}
-			else {
-				failed +=1;
-				if failed == 3 {
-					match read_data.iterator_skip_to_next_frame() {
-						Ok(_) => failed = 0,
-						Err(_) => break,
-					}
-				}
-				#[cfg(debug_assertions)]
-				if self.debug{
-					println!("I am testing this key: {} and got Nothing", Self::as_dna_string(&key) );
-				}
-			}
-			if i == 30 {
-				break;
-			}
-		}
-		let mut res_vec: Vec<_> = res.into_iter().collect();
-		res_vec.retain(|(_, counts)| *counts > 4);
-	    // longest first
-	    res_vec.sort_by(|( (a_key, _a_rel_start), a_counts), ((b_key, _b_rel_start), b_counts)| {
-	    	match b_counts.cmp(&a_counts) {
-		        std::cmp::Ordering::Equal => a_key.cmp(b_key),
-		        other => other,
-		    }
-		});
-
-		res_vec
-    }
-
-	fn query_database_small( &self, seq: &[u8] ) -> Vec<((usize, i32), usize)> {
-    */
 
     fn query_database( &self, seq: &[u8] ) -> Vec<((usize, i32), usize)> {
 		let mut res = HashMap::<(usize, i32), usize>::new();// Vec<i32>>::new();
@@ -618,16 +557,13 @@ impl GenesMapper{
 						break
 					}
 				}
-				#[cfg(debug_assertions)]
-				if self.debug{
-					println!("I got this nw: {nw} and the matches up to now: {}",helper);
-				}
 			};			
 
 		} // end populating helper
+
 		#[cfg(debug_assertions)]
-		if self.debug{
-			//let res_lines = res_vec.iter().map(|obj| format!("{:?}", obj)).collect::<Vec<String>>().join("\n");
+		{
+		//let res_lines = res_vec.iter().map(|obj| format!("{:?}", obj)).collect::<Vec<String>>().join("\n");
 			println!("mapping the read {read_data}\nwe obtained an initial mapping result \n{helper}\nand in the end found \n{:?}",
 				helper.get_best( seq.len()) );
 			println!("#################################################################################");

src/genes_mapper/needleman_wunsch_affine.rs

@@ -383,7 +383,7 @@ impl <'a> NeedlemanWunschAffine {
 		                let mut drop_replaces = 0;
 
 		                // Check nucleotide matches and adjust Cigar vector
-		                while let (Some(nuc1), Some(nuc2)) = (read.get_nucleotide_2bit(read_id.saturating_sub(1)), database.get_nucleotide_2bit(database_id.saturating_sub(1) )) {
+		                while let (Some(_nuc1), Some(_nuc2)) = (read.get_nucleotide_2bit(read_id.saturating_sub(1)), database.get_nucleotide_2bit(database_id.saturating_sub(1) )) {
 
 		                    matching += 1;