very small refactor

nrminor · Apr 10, 2024 · 6d24340 · 6d24340
1 parent b065c94
commit 6d24340
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Showing 2 changed files with 23 additions and 19 deletions.
diff --git a/src/utils.rs b/src/utils.rs
@@ -23,7 +23,7 @@ impl fmt::Display for SeqPlatform {
 }
 
 pub trait RetrieveSampleIds {
- fn retrieve_samples(&self, file_paths: &[Rc<Path>]) -> HashSet<Rc<str>>;
+ fn retrieve_samples(&self, file_paths: &[Rc<Path>]) -> Result<HashSet<Rc<str>>>;
 }
 
 pub fn write_lines(lines: &[String], header: &str, output_prefix: &Option<String>) -> Result<()> {

diff --git a/src/viralrecon.rs b/src/viralrecon.rs
@@ -20,13 +20,13 @@ pub fn find_files(search_dir: &Path, fastq_suffix: &str) -> Result<Vec<Rc<Path>>
 }
 
 impl RetrieveSampleIds for SeqPlatform {
- fn retrieve_samples(&self, file_paths: &[Rc<Path>]) -> HashSet<Rc<str>> {
+ fn retrieve_samples(&self, file_paths: &[Rc<Path>]) -> Result<HashSet<Rc<str>>> {
  match self {
  // handle paired end FASTQ files for Illumina
  SeqPlatform::Illumina => {
- let illumina_pattern = Regex::new(r"_L\d{3}_R\d_\d{3}\.fastq\.gz$").unwrap();
- file_paths
- .into_iter()
+ let illumina_pattern = Regex::new(r"_L\d{3}_R\d_\d{3}\.fastq\.gz$")?;
+ let paired_files = file_paths
+ .iter()
  .map(|path| {
  Rc::from(
  path.file_name()
@@ -36,21 +36,25 @@ impl RetrieveSampleIds for SeqPlatform {
  )
  })
  .map(|x| Rc::from(illumina_pattern.replace_all(&x, "").to_string()))
- .collect()
+ .collect();
+ Ok(paired_files)
  }
  // handle per-barcode single FASTQs for Nanopore
- SeqPlatform::Nanopore => file_paths
- .into_iter()
- .map(|path| {
- Rc::from(
- path.file_name()
- .unwrap_or(OsStr::new(""))
- .to_string_lossy()
- .replace(".fastq.gz", "")
- .as_ref(),
- )
- })
- .collect(),
+ SeqPlatform::Nanopore => {
+ let ont_files = file_paths
+ .iter()
+ .map(|path| {
+ Rc::from(
+ path.file_name()
+ .unwrap_or(OsStr::new(""))
+ .to_string_lossy()
+ .replace(".fastq.gz", "")
+ .as_ref(),
+ )
+ })
+ .collect();
+ Ok(ont_files)
+ }
  }
  }
 }
@@ -129,7 +133,7 @@ pub fn give_a_sheet(
  output_prefix: &Option<String>,
 ) -> Result<()> {
  let fastq_paths = find_files(input_dir, fastq_ext)?;
- let sample_ids: &HashSet<Rc<str>> = &platform.retrieve_samples(&fastq_paths);
+ let sample_ids = &platform.retrieve_samples(&fastq_paths)?;
  let lines = concat_lines(sample_ids, &fastq_paths, platform);
  let header = "sample,fastq_1,fastq_2";
  write_lines(&lines, header, output_prefix)