make clippy happy

src/collate.rs

@@ -250,7 +250,7 @@ fn correct_unmapped_counts(
         .expect("couldn't serialize corrected unmapped bc count.");
 }
 
-#[allow(clippy::too_many_arguments)]
+#[allow(clippy::too_many_arguments, clippy::manual_clamp)]
 pub fn collate_with_temp<P1, P2>(
     input_dir: P1,
     rad_dir: P2,
@@ -331,7 +331,7 @@ where
 
         let cm_path = parent.join("collate.json");
         let mut cm_file =
-            std::fs::File::create(&cm_path).context("could not create metadata file.")?;
+            std::fs::File::create(cm_path).context("could not create metadata file.")?;
 
         let cm_info_string =
             serde_json::to_string_pretty(&collate_meta).context("could not format json.")?;
@@ -536,7 +536,7 @@ where
     let min_rec_len = 24usize; // smallest size an individual record can be loaded in memory
     let max_rec = max_records as usize;
     let num_buckets = temp_buckets.len();
-    let num_threads = n_workers as usize;
+    let num_threads = n_workers;
     let loc_buffer_size = (min_rec_len + (most_ambig_record * 4_usize) - 4_usize).max(
         (1000_usize.max((min_rec_len * max_rec) / (num_buckets * num_threads))).min(262_144_usize),
     ); //131072_usize);
@@ -682,7 +682,7 @@ where
         let observed = temp_bucket.2.num_records_written.load(Ordering::SeqCst);
         assert_eq!(expected, observed);
 
-        let md = std::fs::metadata(parent.join(&format!("bucket_{}.tmp", i)))?;
+        let md = std::fs::metadata(parent.join(format!("bucket_{}.tmp", i)))?;
         let expected_bytes = temp_bucket.2.num_bytes_written.load(Ordering::SeqCst);
         let observed_bytes = md.len();
         assert_eq!(expected_bytes, observed_bytes);
@@ -691,7 +691,7 @@ where
     //std::process::exit(1);
 
     // to hold the temp buckets threads will process
-    let slack = ((n_workers / 2) as usize).max(1_usize);
+    let slack = (n_workers / 2).max(1_usize);
     let temp_bucket_queue_size = slack + n_workers;
     let fq = Arc::new(ArrayQueue::<(
         u32,
@@ -740,7 +740,7 @@ where
                     buckets_remaining.fetch_sub(1, Ordering::SeqCst);
                     cmap.clear();
 
-                    let fname = parent.join(&format!("bucket_{}.tmp", temp_bucket.2.bucket_id));
+                    let fname = parent.join(format!("bucket_{}.tmp", temp_bucket.2.bucket_id));
                     // create a new handle for reading
                     let tfile = std::fs::File::open(&fname).expect("couldn't open temporary file.");
                     let mut treader = BufReader::new(tfile);

src/convert.rs

@@ -305,7 +305,7 @@ where
     let expected_bar_length = bam_bytes / ((buf_limit as u64) * 24);
     // let expected_bar_length = 50u64 ;// bam_bytes / ((buf_limit as u64) * 24);
 
-    let pbar_inner = ProgressBar::new(expected_bar_length as u64);
+    let pbar_inner = ProgressBar::new(expected_bar_length);
     pbar_inner.set_style(sty);
     pbar_inner.tick();
 

src/em.rs

@@ -41,7 +41,7 @@ pub enum EmInitType {
 
 #[allow(dead_code)]
 fn mean(data: &[f64]) -> Option<f64> {
-    let sum = data.iter().sum::<f64>() as f64;
+    let sum = data.iter().sum::<f64>();
     let count = data.len();
 
     match count {
@@ -57,7 +57,7 @@ fn std_deviation(data: &[f64]) -> Option<f64> {
             let variance = data
                 .iter()
                 .map(|value| {
-                    let diff = data_mean - (*value as f64);
+                    let diff = data_mean - *value;
 
                     diff * diff
                 })
@@ -389,7 +389,7 @@ pub fn em_optimize(
 
                 max_rel_diff = match rel_diff > max_rel_diff as f32 {
                     true => rel_diff as f64,
-                    false => max_rel_diff as f64,
+                    false => max_rel_diff,
                 };
 
                 if rel_diff > REL_DIFF_TOLERANCE {

src/infer.rs

@@ -87,7 +87,7 @@ pub fn infer(
     let num_genes = global_eq_classes.num_genes;
 
     let usa_offsets = if usa_mode {
-        Some(((num_genes / 3) as usize, (2 * num_genes / 3) as usize))
+        Some((num_genes / 3, (2 * num_genes / 3)))
     } else {
         None
     };
@@ -277,7 +277,7 @@ pub fn infer(
 
                         // fill out the triplet matrix in memory
                         for (ind, val) in expressed_ind.iter().zip(expressed_vec.iter()) {
-                            writer.add_triplet(row_index as usize, *ind, *val);
+                            writer.add_triplet(row_index, *ind, *val);
                         }
                         /*
                         writeln!(
@@ -391,7 +391,7 @@ pub fn infer(
     let output_matrix_path = output_path.join("quants_mat.mtx");
     let writer_deref = trimat.lock();
     let writer = &*writer_deref.unwrap();
-    sprs::io::write_matrix_market(&output_matrix_path, writer)?;
+    sprs::io::write_matrix_market(output_matrix_path, writer)?;
 
     Ok(())
 }

src/main.rs

@@ -44,6 +44,7 @@ fn gen_random_kmer(k: usize) -> String {
     s
 }
 
+#[allow(clippy::manual_clamp)]
 fn main() -> anyhow::Result<()> {
     let num_hardware_threads = num_cpus::get() as u32;
     let max_num_threads: String = (num_cpus::get() as u32).to_string();

src/pugutils.rs

@@ -201,7 +201,7 @@ pub fn extract_graph(
 
                 // recall that we processed this eq class as a neighbor of eqid
                 hset[*eq2id as usize] = 1;
-                idxvec.push(*eq2id as u32);
+                idxvec.push(*eq2id);
                 let eq2 = &eqmap.eqc_info[*eq2id as usize];
 
                 // compare all the umis between eqid and eq2id

src/quant.rs

@@ -216,7 +216,7 @@ fn write_eqc_counts(
 
     // and write it to file.
     let mtx_path = output_path.join("geqc_counts.mtx");
-    sprs::io::write_matrix_market(&mtx_path, &eqmat).context("could not write geqc_counts.mtx")?;
+    sprs::io::write_matrix_market(mtx_path, &eqmat).context("could not write geqc_counts.mtx")?;
 
     // write the sets of genes that define each eqc
     let gn_eq_path = output_path.join("gene_eqclass.txt.gz");
@@ -248,7 +248,7 @@ fn write_eqc_counts(
         // offset for unspliced gene ids
         let unspliced_offset = (num_genes / 3) as u32;
         // offset for ambiguous gene ids
-        let ambig_offset = (2 * unspliced_offset) as u32;
+        let ambig_offset = 2 * unspliced_offset;
         // to hold the gene labels as we write them.
         let mut gl;
 
@@ -603,13 +603,12 @@ pub fn do_quantify<T: Read>(mut br: T, quant_opts: QuantOpts) -> anyhow::Result<
     };
 
     let usa_offsets = if usa_mode {
-        Some(((num_rows / 3) as usize, (2 * num_rows / 3) as usize))
+        Some((num_rows / 3, (2 * num_rows / 3)))
     } else {
         None
     };
 
-    let trimat =
-        sprs::TriMatI::<f32, u32>::with_capacity((num_cells as usize, num_rows as usize), tmcap);
+    let trimat = sprs::TriMatI::<f32, u32>::with_capacity((num_cells as usize, num_rows), tmcap);
 
     let bc_writer = Arc::new(Mutex::new(QuantOutputInfo {
         barcode_file: BufWriter::new(bc_file),
@@ -676,11 +675,11 @@ pub fn do_quantify<T: Read>(mut br: T, quant_opts: QuantOpts) -> anyhow::Result<
             EqMapType::GeneLevel => {
                 // get the max spliced gene ID and add 1 to get the unspliced ID
                 // and another 1 to get the size.
-                (gene_name_to_id
+                gene_name_to_id
                     .values()
                     .max()
                     .expect("gene name to id map should not be empty.")
-                    + 2) as u32
+                    + 2
             }
         };
 
@@ -870,8 +869,7 @@ pub fn do_quantify<T: Read>(mut br: T, quant_opts: QuantOpts) -> anyhow::Result<
                                     let g = pugutils::extract_graph(&eq_map, pug_exact_umi, &log);
                                     // for the PUG resolution algorithm, set the hasher
                                     // that will be used based on the cell barcode.
-                                    let s =
-                                        ahash::RandomState::with_seeds(bc as u64, 7u64, 1u64, 8u64);
+                                    let s = ahash::RandomState::with_seeds(bc, 7u64, 1u64, 8u64);
                                     let pug_stats = pugutils::get_num_molecules(
                                         &g,
                                         &eq_map,
@@ -1129,7 +1127,7 @@ pub fn do_quantify<T: Read>(mut br: T, quant_opts: QuantOpts) -> anyhow::Result<
                             } else {
                                 // fill out the triplet matrix in memory
                                 for (ind, val) in expressed_ind.iter().zip(expressed_vec.iter()) {
-                                    writer.trimat.add_triplet(row_index as usize, *ind, *val);
+                                    writer.trimat.add_triplet(row_index, *ind, *val);
                                 }
                             }
                             writeln!(
@@ -1266,7 +1264,7 @@ pub fn do_quantify<T: Read>(mut br: T, quant_opts: QuantOpts) -> anyhow::Result<
         // now remove it
         fs::remove_file(&mat_path)?;
         let mtx_path = output_matrix_path.join("quants_mat.mtx");
-        sprs::io::write_matrix_market(&mtx_path, &writer.trimat)?;
+        sprs::io::write_matrix_market(mtx_path, &writer.trimat)?;
     }
 
     let pb_msg = format!(