changes

src/lib.rs

@@ -1,15 +1,16 @@
 use anyhow::{Ok, Result};
 use log::info;
 use minimap2::{Aligner, Mapping};
+use noodles_fasta as fasta;
 use rust_htslib::bam::{self, Record};
 use std::{
     collections::{HashMap, VecDeque},
     fmt,
-    fs::{File, self},
-    io::{BufWriter, Write}, process::{Command, Stdio},
+    fs::{self, File},
+    io::{BufWriter, Write},
+    process::{Command, Stdio},
 };
 use uuid::Uuid;
-use noodles_fasta as fasta;
 
 #[derive(Debug, Clone)]
 pub struct Genome {
@@ -329,10 +330,16 @@ impl Contig {
         fs::create_dir_all(contig_dir.clone())?;
 
         let fasta_path = format!("{contig_dir}/contig.fa");
-        write_fasta(&fasta_path, &vec![( self.id.clone(), self.sequence.clone() )]);
-
-        let reads_path = format!("{contig_dir}/reads.fq");
-        write_fastq(&reads_path, &self.supporting_records)?;
+        write_fasta(&fasta_path, &vec![(self.id.clone(), self.sequence.clone())]);
+
+        let reads_path = format!("{contig_dir}/reads.fa");
+        let n_reads = self.supporting_records.clone().into_iter().map(|r| {
+            (
+                String::from_utf8(r.qname().to_vec()).unwrap(),
+                String::from_utf8(r.seq().as_bytes()).unwrap(),
+            )
+        }).collect();
+        write_fasta(&reads_path, &n_reads);
 
         let bam_path = format!("{contig_dir}/{}.bam", self.id);
         create_bam(&fasta_path, &reads_path, &bam_path)?;