Fix compile error caused by removal of helper function

src/group.rs

@@ -1,5 +1,5 @@
 use crate::duplicates::DuplicateMap;
-use crate::io::{iter_duplicates, until_err, ReadType};
+use crate::io::{iter_duplicates, ReadType};
 
 use std::io::prelude::*;
 
@@ -16,45 +16,31 @@ use anyhow::Result;
 /// # Returns
 ///
 /// * `Result<()>` - Returns `Ok(())` if successful, or an error if an error occurs during processing.
-pub fn group(
-    input: &str,
-    writer: &mut impl Write,
-    duplicates: DuplicateMap,
-) -> Result<()> {
-    // Start with a placeholder error object. This will be mutated if there are errors during
-    // iteration through the reads.
-    let mut err = Ok(());
-
-    let duplicate_iterator = iter_duplicates(
-        input,
-        duplicates,
-        false,
-    )?;
+pub fn group(input: &str, writer: &mut impl Write, duplicates: DuplicateMap) -> Result<()> {
+    let mut duplicate_iterator = iter_duplicates(input, duplicates, 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);
+    let mut first = true;
+    while let Some(elem) = duplicate_iterator.next() {
+        count += 1;
+        if count % 500000 == 0 {
+            info!("Processed: {} reads", count);
+        }
+
+        let mut group = elem?;
+        let group_size = group.records.len();
+        for (idx, rec) in group.records.iter_mut().enumerate() {
+            if first {
+                first = false
+            } else {
+                writer.write_all(b"\n")?
             }
 
-            for rec in group.records.iter() {
-                // write to the output file
-                crate::io::write_read(
-                    writer,
-                    rec,
-                    &group,
-                    ReadType::Original,
-                    true,
-                )?
-            }
-
-            Ok(())
-        })?;
+            rec.add_metadata(group.index, ReadType::Original, idx + 1, group_size, 0.0);
+            rec.write_fastq(writer)?;
+        }
+    }
 
-    err
+    Ok(())
 }

src/io.rs

@@ -73,6 +73,7 @@ impl Record {
         write!(self.id, " UT:Z:{read_type_label} UG:i:{umi_group}")
             .expect("String writing should not error");
 
+        // don't report the group average quality if the readtype is Original or Ignored
         if !matches!(read_type, ReadType::Original | ReadType::Ignored) {
             write!(self.id, " QL:f:{avg_qual:.2}").expect("String writing should not error");
         }
@@ -268,32 +269,3 @@ where
 
     Some(Ok(rec))
 }
-
-/// Utility function to extract the error from an iterator and stop iteration immediately. Useful
-/// for iterators which yield a Result<T>.
-///
-/// # Returns
-///
-/// This function returns an `Option<T>`. If the item is `Ok`, it returns `Some(T)`.
-/// If the item is `Err`, it updates `err` with the error and returns `None`.
-///
-/// # Example
-/// ```
-/// let mut err = Ok(());
-/// let items = vec![Ok(1), Ok(2), Err(anyhow!("error")), Ok(3)];
-/// let results: Vec<_> = items
-///   .into_iter()
-///   .scan(&mut err, until_err)
-///   .collect();
-/// assert_eq!(results, vec![1, 2]);
-/// assert!(err.is_err());
-/// ```
-pub fn until_err<T>(err: &mut &mut anyhow::Result<()>, item: anyhow::Result<T>) -> Option<T> {
-    match item {
-        Ok(item) => Some(item),
-        Err(e) => {
-            **err = Err(e);
-            None
-        }
-    }
-}