Tests work fine again.

src/analysis/gene_mapper.rs

@@ -498,12 +498,13 @@ impl AnalysisGeneMapper{
 		                        	report
 		                        ){
 		                        	report.pcr_duplicates += 1;
-		                        	match minimal_sam.to_sam_line( &data[i].1, gene_id, cell_seq, umi_seq, &self.genes ) {
-			                        	Some(sam_line) => bam.push( sam_line ),
-			                        	None => {
-			                        		eprintln!("There has been an error in the minimal_sam.to_sam_line function - please check what went wrong with this sequence:\n{}.",&data[i].1 );
-			                        	}
-			                        }
+		                        }
+		                        // add it whether it is a duplicate or not
+		                        match minimal_sam.to_sam_line( &data[i].1, gene_id, cell_seq, umi_seq, &self.genes ) {
+		                        	Some(sam_line) => bam.push( sam_line ),
+		                        	None => {
+		                        		eprintln!("There has been an error in the minimal_sam.to_sam_line function - please check what went wrong with this sequence:\n{}.",&data[i].1 );
+		                        	}
 		                        }
 		                    },
 		                    Err(MappingError::NoMatch) => {

src/bin/check_read_gene_mapper.rs

@@ -151,7 +151,7 @@ fn main() {
 
     //worker.write_data( opts.outpath, &mut results, opts.min_umi );
 
-
+    println!("{}",results.log_str());
 
     match now.elapsed() {
         Ok(elapsed) => {

src/genes_mapper/genes_mapper.rs

@@ -546,6 +546,7 @@ impl GenesMapper{
 		let res_vec = self.query_database( seq );
 
 		if res_vec.is_empty() {
+			#[cfg(debug_assertions)]
 			if self.debug{
 				println!("No matching gene found - cause: Not enough keys matching to a single gene");
 			}

src/singlecelldata/singlecelldata.rs

@@ -519,6 +519,10 @@ impl SingleCellData{
         ret
     }
 
+    pub fn passing_cells( &self) -> usize {
+        self.passing
+    }
+
     pub fn n_reads( &mut self, genes:&IndexedGenes, names: &Vec<String> ) -> usize {
         let mut count = 0;
 

tests/analysis_gene_mapper_internals_R1.rs

@@ -36,7 +36,11 @@ mod tests {
 	    		assert_eq!( sam_strings.len(), 0, "I go no result for the search" );
 	    	},
 	    	None=> {
-	    		assert_eq!(sam_strings[0], sam_line, "We got the expected sam line?");
+	    		if sam_strings.len() > 0 {
+	    			assert_eq!(sam_strings[0], sam_line, "We got the expected sam line?");
+	    		}else {
+	    			panic!("I expected a sam line in return and got nothing?!");
+	    		}
 	    	}
 	    }
 	}

tests/test_mapping_efficiency.rs

@@ -146,5 +146,5 @@ fn test_quantify_rhapsody_multi_bad_seq2() {
 
     let stdout = std::str::from_utf8( &output.stdout).unwrap();
 
-    assert!( stdout.contains( "No matching gene found"), "Gene detected!: {stdout}");
+    assert!( stdout.contains( "100.00% with cell_id, 0.00% with gene_id 0.00% multimapper"), "Gene detected!: {stdout}");
 }