Formatting adjustments with Clippy

src/call.rs

@@ -1,15 +1,12 @@
-use crate::duplicates::{DuplicateMap, RecordIdentifier};
-use crate::io::{iter_duplicates, until_err, write_read, ReadType, Record, UMIGroup};
+use crate::duplicates::DuplicateMap;
+use crate::io::{iter_duplicates, until_err, ReadType, Record, UMIGroup};
 
-use needletail::parser::{FastqReader, FastxReader, SequenceRecord};
 use spoa::{AlignmentEngine, AlignmentType};
 
-use std::fs::File;
 use std::io::prelude::*;
-use std::io::{Cursor, Seek, SeekFrom};
-use std::process::{Command, Stdio};
+use std::io::Cursor;
 
-use anyhow::{anyhow, Context, Result};
+use anyhow::Result;
 
 use crate::io;
 use pariter::IteratorExt as _;
@@ -96,7 +93,7 @@ fn call_record(group: UMIGroup, output_originals: bool) -> Vec<u8> {
     // for singletons, the read is its own consensus
     if length == 1 {
         let record = &group.records[0];
-        io::write_read(&mut output, record, &group, ReadType::CONSENSUS, false).unwrap();
+        io::write_read(&mut output, record, &group, ReadType::Consensus, false).unwrap();
         return output.into_inner();
     }
 
@@ -109,7 +106,7 @@ fn call_record(group: UMIGroup, output_originals: bool) -> Vec<u8> {
     for record in group.records.iter() {
         if output_originals {
             // Write the original reads as well
-            io::write_read(&mut output, record, &group, ReadType::ORIGINAL, false).unwrap();
+            io::write_read(&mut output, record, &group, ReadType::Original, false).unwrap();
         }
 
         // Align to the graph
@@ -135,7 +132,7 @@ fn call_record(group: UMIGroup, output_originals: bool) -> Vec<u8> {
         qual: "".to_string(),
     };
 
-    io::write_read(&mut output, &consensus, &group, ReadType::CONSENSUS, false).unwrap();
+    io::write_read(&mut output, &consensus, &group, ReadType::Consensus, false).unwrap();
 
     output.into_inner()
 }

src/duplicates.rs

@@ -16,7 +16,7 @@ pub struct RecordIdentifier {
 
 impl std::fmt::Display for RecordIdentifier {
     fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
-        if self.tail.len() == 0 {
+        if self.tail.is_empty() {
             f.write_str(&self.head)
         } else {
             write!(f, "{}_{}", self.head, self.tail)

src/generate_index.rs

@@ -8,7 +8,7 @@ use regex::Regex;
 use crate::generate_index::IndexGenerationErr::{InvalidClusterRow, RowNotInClusters};
 use anyhow::{bail, Context, Result};
 use needletail::parser::SequenceRecord;
-use needletail::{FastxReader, Sequence};
+use needletail::FastxReader;
 use thiserror::Error;
 
 use crate::file::FastqFile;
@@ -127,12 +127,10 @@ fn iter_lines_with_cluster_file<W: Write>(
     for result in clusters.records() {
         let record = result?;
 
-        let len = record.len();
-
         let read_id = record[0].to_string();
         let identifier = match record.len() {
             2 => record[1].to_string(),
-            3 => format!("{}_{}", record[1].to_string(), record[2].to_string()),
+            3 => format!("{}_{}", &record[1], &record[2]),
             _ => bail!(InvalidClusterRow {row: record.as_slice().to_string()})
         };
 
@@ -165,7 +163,7 @@ fn iter_lines_with_cluster_file<W: Write>(
         };
         info.matched_read_count += 1;
 
-        total_quality += write_read(wtr, &rec, &identifier, position)?;
+        total_quality += write_read(wtr, &rec, identifier, position)?;
         total_len += rec.num_bases();
     }
 
@@ -239,7 +237,7 @@ pub fn construct_index(
         None => { iter_lines_with_regex(reader, &mut wtr, &re, skip_unmatched, file_info) }
         Some(filepath) => {
             let mut cluster_rdr = csv::ReaderBuilder::new()
-                .delimiter(';' as u8)
+                .delimiter(b';')
                 .has_headers(false)
                 .from_path(filepath)?;
 

src/group.rs

@@ -31,17 +31,24 @@ pub fn group(
         false,
     )?;
 
+    let mut count = 0usize;
+
     duplicate_iterator
         // iterate until an error is found, writing into &err
         .scan(&mut err, until_err)
         .try_for_each(|group| -> Result<()> {
+            count += 1;
+            if count % 500000 == 0 {
+                info!("Processed: {} reads", count);
+            }
+
             for rec in group.records.iter() {
                 // write to the output file
                 crate::io::write_read(
                     writer,
-                    &rec,
+                    rec,
                     &group,
-                    ReadType::ORIGINAL,
+                    ReadType::Original,
                     true,
                 )?
             }

src/io.rs

@@ -6,8 +6,8 @@ use std::fs::File;
 use std::io::{Seek, SeekFrom, Write};
 
 pub enum ReadType {
-    CONSENSUS,
-    ORIGINAL,
+    Consensus,
+    Original,
 }
 
 pub struct Record {
@@ -64,7 +64,7 @@ pub fn get_read_at_position(
     Ok(Record {
         id: String::from_utf8(rec.id().to_vec())?,
         seq: String::from_utf8(rec.seq().to_vec())?,
-        qual: String::from_utf8(rec.qual().unwrap_or_else(|| &[]).to_vec())?,
+        qual: String::from_utf8(rec.qual().unwrap_or(&[]).to_vec())?,
     })
 }
 
@@ -80,7 +80,8 @@ pub fn get_read_at_position(
 /// This function will return an error if:
 /// * The file cannot be opened.
 /// * The record cannot be read at the specified position.
-/// The iterator yield Some(Err) if:
+///
+/// The iterator yields Some(Err) if:
 /// * There are issues reading the read at at the specified position. See the documentation for
 ///   `get_read_at_position` for more.
 pub fn iter_duplicates(
@@ -176,8 +177,8 @@ pub fn write_read(
     fastq: bool,
 ) -> std::io::Result<()> {
     let read_type_label = match read_type {
-        ReadType::CONSENSUS => { "CONSENSUS" }
-        ReadType::ORIGINAL => { "ORIGINAL" }
+        ReadType::Consensus => { "CONSENSUS" }
+        ReadType::Original => { "ORIGINAL" }
     };
 
     if fastq {

src/main.rs

@@ -1,5 +1,5 @@
 // disable unused code warnings for dev builds
-#![cfg_attr(debug_assertions, allow(dead_code, unused_imports, unused_variables))]
+// #![cfg_attr(debug_assertions, allow(dead_code, unused_imports, unused_variables))]
 
 extern crate env_logger;
 #[macro_use]

src/summary.rs

@@ -1,7 +1,6 @@
 use crate::duplicates;
 use anyhow::{Context, Result};
 use serde_json::json;
-use std::collections::HashMap;
 
 // include the template HTML file at compile time as a string literal
 const TEMPLATE_HTML: &str = include_str!("summary_template.html");
@@ -24,8 +23,8 @@ pub fn summarize(index: &str, output: &str) -> Result<()> {
     );
 
     let file = std::fs::File::create(output)?;
-    let mut reg = handlebars::Handlebars::new();
-    reg.render_template_to_write(TEMPLATE_HTML, &data, file);
+    let reg = handlebars::Handlebars::new();
+    reg.render_template_to_write(TEMPLATE_HTML, &data, file)?;
 
     Ok(())
 }