behold the glory of clippy

src/main.rs

@@ -25,7 +25,7 @@ fn main() -> Result<()> {
  expected_cells,
  output_prefix,
  }) => {
- scrnaseq::give_a_sheet(input_dir, fastq_ext, &expected_cells, output_prefix)?;
+ scrnaseq::give_a_sheet(input_dir, fastq_ext, expected_cells, output_prefix)?;
  }
  None => {
  eprintln!("{}\n", cli::INFO);

src/scrnaseq.rs

@@ -10,7 +10,7 @@ fn retrieve_samples(file_paths: &[Rc<Path>]) -> HashSet<Rc<str>> {
  let illumina_pattern = Regex::new(r"_L\d{3}_R\d_\d{3}\.fastq\.gz$").unwrap();
 
  file_paths
- .into_iter()
+ .iter()
  .map(|path| {
  Rc::from(
  path.file_name()
@@ -38,21 +38,18 @@ fn collect_per_sample(
 ) -> Result<String> {
  // figure out which FASTQ files go with the provided sample_id
  let sample_fastqs: Vec<&str> = fastq_paths
- .into_iter()
- .map(|x| match x.to_str() {
- Some(path_str_slice) => path_str_slice,
- None => &"",
- })
+ .iter()
+ .map(|x| x.to_str().unwrap_or(""))
  .filter(|x| x.contains(sample_id.as_ref()))
  .collect();
 
  // pull out the R1 and R2 FASTQ files
- let fastq1: &str = &sample_fastqs
+ let fastq1 = sample_fastqs
  .iter()
  .find(|x| x.contains("R1"))
  .ok_or("No fastq file with 'R1' found")
  .unwrap();
- let fastq2: &str = &sample_fastqs
+ let fastq2 = sample_fastqs
  .iter()
  .find(|x| x.contains("R2"))
  .ok_or("No fastq file with 'R2' found")
@@ -61,7 +58,7 @@ fn collect_per_sample(
  let cell_str = expected_cells.to_string();
 
  // instantiate an illumina line and return it
- Ok(vec![sample_id, fastq1, fastq2, &cell_str].join(","))
+ Ok([sample_id.as_ref(), fastq1, fastq2, &cell_str].join(","))
 }
 
 fn concat_lines(

src/utils.rs

@@ -37,7 +37,7 @@ pub fn write_lines(lines: &[String], header: &str, output_prefix: &Option<String
 
  writeln!(buf_writer, "{}", header)?;
  lines
- .into_iter()
+ .iter()
  .try_for_each(|line| writeln!(buf_writer, "{}", line))?;
 
  Ok(())

src/viralrecon.rs

@@ -77,39 +77,36 @@ impl CollectByPlatform for SeqPlatform {
  SeqPlatform::Illumina => {
  // figure out which FASTQ files go with the provided sample_id
  let sample_fastqs: Vec<&str> = fastq_paths
- .into_iter()
- .map(|x| match x.to_str() {
- Some(path_str_slice) => path_str_slice,
- None => &"",
- })
+ .iter()
+ .map(|x| x.to_str().unwrap_or(""))
  .filter(|x| x.contains(sample_id.as_ref()))
  .collect();
 
  // pull out the R1 and R2 FASTQ files
- let fastq1: &str = &sample_fastqs
+ let fastq1 = sample_fastqs
  .iter()
  .find(|x| x.contains("R1"))
  .ok_or("No fastq file with 'R1' found")
  .unwrap();
- let fastq2: &str = &sample_fastqs
+ let fastq2 = sample_fastqs
  .iter()
  .find(|x| x.contains("R2"))
  .ok_or("No fastq file with 'R2' found")
  .unwrap();
 
  // instantiate an illumina line and return it
- Ok(vec![sample_id, fastq1, fastq2].join(","))
+ Ok([sample_id.as_ref(), fastq1, fastq2].join(","))
  }
  SeqPlatform::Nanopore => {
  // pull out the barcode
- let barcode = if sample_id.starts_with("0") {
+ let barcode = if sample_id.starts_with('0') {
  sample_id.replace("barcode", "").chars().skip(1).collect()
  } else {
  sample_id.replace("barcode", "")
  };
 
  // instantiate a Nanopore line and return it
- Ok(vec![sample_id.as_ref(), &barcode].join(","))
+ Ok([sample_id.as_ref(), &barcode].join(","))
  }
  }
  }