fixes

Author: nh13

src/bin/commands/demux.rs

@@ -93,7 +93,7 @@ impl ReadSet {
     const SPACE: u8 = b' ';
     const COLON: u8 = b':';
     const PLUS: u8 = b'+';
-    const READ_NUMBERS: &[u8] = &[b'1', b'2', b'3', b'4', b'5', b'6', b'7', b'8'];
+    const READ_NUMBERS: &[u8] = b"12345678";
 
     /// Produces an iterator over references to the template segments stored in this ``ReadSet``.
     fn template_segments(&self) -> SegmentIter {
@@ -217,7 +217,7 @@ impl ReadSet {
                 if read_num < Self::READ_NUMBERS.len() {
                     writer.write_all(&[Self::READ_NUMBERS[read_num - 1]])?;
                     write!(writer, ":N:0:")?;
-                } else{
+                } else {
                     write!(writer, "{}:N:0:", read_num)?;
                 }
             }
@@ -247,7 +247,7 @@ impl ReadSet {
 
                     if read_num < Self::READ_NUMBERS.len() {
                         writer.write_all(&[Self::READ_NUMBERS[read_num - 1], b':'])?;
-                    } else{
+                    } else {
                         write!(writer, "{}:", read_num)?;
                     }
                     writer.write_all(remainder)?;
@@ -546,6 +546,7 @@ impl DemuxMetric {
 ///    mismatches (see `--max-mismatches`).
 /// 2. The difference between number of mismatches in the best and second best barcodes is greater
 ///    than or equal to the minimum mismatch delta (`--min-mismatch-delta`).
+///
 /// The expected barcode sequence may contains Ns, which are not counted as mismatches regardless
 /// of the observed base (e.g. the expected barcode `AAN` will have zero mismatches relative to
 /// both the observed barcodes `AAA` and `AAN`).
@@ -754,7 +755,7 @@ impl Demux {
             let mut new_sample_barcode_writers = None;
             let mut new_molecular_barcode_writers = None;
 
-            for (optional_ws, target) in vec![
+            for (optional_ws, target) in [
                 (template_writers, &mut new_template_writers),
                 (barcode_writers, &mut new_sample_barcode_writers),
                 (mol_writers, &mut new_molecular_barcode_writers),
@@ -907,7 +908,7 @@ impl Command for Demux {
         );
 
         let mut fq_iterators = fq_sources
-            .zip(self.read_structures.clone().into_iter())
+            .zip(self.read_structures.clone())
             .map(|(source, read_structure)| {
                 ReadSetIterator::new(read_structure, source, self.skip_reasons.clone())
                     .read_ahead(1000, 1000)
@@ -1194,6 +1195,7 @@ mod tests {
             skip_reasons: vec![],
         };
         let demux_result = demux_inputs.execute();
+        #[allow(clippy::permissions_set_readonly_false)]
         permissions.set_readonly(false);
         fs::set_permissions(tmp.path(), permissions).unwrap();
         demux_result.unwrap();
@@ -1888,11 +1890,11 @@ mod tests {
         let read_structures =
             vec![ReadStructure::from_str("+T").unwrap(), ReadStructure::from_str("7B").unwrap()];
 
-        let records = vec![
+        let records = [
             vec!["AAAAAAA", &SAMPLE1_BARCODE[0..7]], // barcode too short
             vec!["CCCCCCC", SAMPLE1_BARCODE],        // barcode the correct length
             vec!["", SAMPLE1_BARCODE],               // template basese too short
-            vec!["G", SAMPLE1_BARCODE],              // barcode the correct length
+            vec!["G", SAMPLE1_BARCODE],
         ];
 
         let input_files = vec![
@@ -1924,11 +1926,11 @@ mod tests {
         let read_structures =
             vec![ReadStructure::from_str("+T").unwrap(), ReadStructure::from_str("7B").unwrap()];
 
-        let records = vec![
+        let records = [
             vec!["AAAAAAA", &SAMPLE1_BARCODE[0..7]], // barcode too short
             vec!["CCCCCCC", SAMPLE1_BARCODE],        // barcode the correct length
             vec!["", SAMPLE1_BARCODE],               // template basese too short
-            vec!["G", SAMPLE1_BARCODE],              // barcode the correct length
+            vec!["G", SAMPLE1_BARCODE],
         ];
 
         let input_files = vec![

src/lib/barcode_matching.rs

@@ -85,7 +85,9 @@ impl BarcodeMatcher {
             );
         }
         let mut count: usize = 0;
-        for (&expected_base, &observed_base) in sample.barcode_bytes.iter().zip(observed_bases.iter()) {
+        for (&expected_base, &observed_base) in
+            sample.barcode_bytes.iter().zip(observed_bases.iter())
+        {
             if expected_base != observed_base && !byte_is_nocall(expected_base) {
                 count += 1;
             }

src/lib/samples.rs

@@ -297,11 +297,7 @@ mod tests {
         let barcode = "GATTACA".to_owned();
         let ordinal = 0;
         let sample = Sample::new(ordinal, name.clone(), barcode.clone());
-        assert_eq!(
-            Sample { sample_id: name, barcode, ordinal },
-            sample,
-            "Sample differed from expectation"
-        );
+        assert_eq!(Sample::new(ordinal, name, barcode), sample, "Sample differed from expectation");
     }
 
     // ############################################################################################