actually correct based on overlap

src/bin/commands/trimmer.rs

@@ -2,6 +2,7 @@ use crate::commands::command::Command;
 use anyhow::{Error, Result};
 use clap::Parser;
 use fgoxide::io::Io;
+use fqtk_lib::pair_overlap;
 use log::info;
 use pooled_writer::{bgzf::BgzfCompressor, Pool, PoolBuilder, PooledWriter};
 use seq_io::fastq::{OwnedRecord, Reader as FastqReader, Record};
@@ -25,7 +26,7 @@ pub(crate) struct Trimmer {
     /// Minimum difference in base-quality for one read to correct an overlapping
     /// base from the other read.
     #[clap(long, short = 'd', default_value = "15")]
-    overlap_min_bq_delta: usize,
+    overlap_min_bq_delta: u8,
 
     /// Minimum pair overlap length to attempt correction.
     #[clap(long, short = 'l', default_value = "50")]
@@ -109,10 +110,20 @@ impl Command for Trimmer {
         let f2 = readers.remove(0);
 
         for (r1, r2) in f1.into_records().zip(f2.into_records()) {
-            let r1 = r1?;
-            let r2 = r2?;
+            let mut r1 = r1?;
+            let mut r2 = r2?;
+
+            if let Some(overlap) = pair_overlap::find_overlap(
+                r1.seq(),
+                r2.seq(),
+                self.overlap_min_len,
+                self.overlap_max_error_rate,
+            ) {
+                overlap.correct(&mut r1, &mut r2, self.overlap_min_bq_delta, true);
+            }
+
             r1.write(&mut writers[0])?;
-            r2.write(&mut writers[0])?;
+            r2.write(&mut writers[1])?;
         }
 
         writers.into_iter().try_for_each(|w| w.close())?;