changes

src/lib.rs

@@ -334,12 +334,17 @@ impl Contig {
         write_fai(&fasta_path);
 
         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();
+        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);
@@ -349,12 +354,32 @@ impl Contig {
         match &self.contig_ref {
             ContigRef::Chimeric((a, b)) => {
                 let d = vec![
-                    (self.id.clone(), a.query_start, a.query_end, format!("{}:{}-{}", a.target_name.clone().unwrap(), a.target_start, a.target_end)),
-                    (self.id.clone(), b.query_start, b.query_end, format!("{}:{}-{}", b.target_name.clone().unwrap(), b.target_start, b.target_end))
+                    (
+                        self.id.clone(),
+                        a.query_start,
+                        a.query_end,
+                        format!(
+                            "{}:{}-{}",
+                            a.target_name.clone().unwrap(),
+                            a.target_start,
+                            a.target_end
+                        ),
+                    ),
+                    (
+                        self.id.clone(),
+                        b.query_start,
+                        b.query_end,
+                        format!(
+                            "{}:{}-{}",
+                            b.target_name.clone().unwrap(),
+                            b.target_start,
+                            b.target_end
+                        ),
+                    ),
                 ];
                 write_bed(&bed_path, &d)?;
-            },
-            _ => ()
+            }
+            _ => (),
         }
 
         Ok(())
@@ -438,7 +463,16 @@ pub fn write_bed(path: &str, d: &Vec<(String, i32, i32, String)>) -> Result<()>
     let file = File::create(path).unwrap();
     let mut writer = BufWriter::new(file);
     for (chr, start, end, value) in d.iter() {
-        let row = format!("{}\n", vec![chr.to_string(), start.to_string(), end.to_string(), value.to_string()].join("\t"));
+        let row = format!(
+            "{}\n",
+            vec![
+                chr.to_string(),
+                start.to_string(),
+                end.to_string(),
+                value.to_string()
+            ]
+            .join("\t")
+        );
         writer.write_all(row.as_bytes())?;
     }
     Ok(())
@@ -482,7 +516,11 @@ pub fn write_fasta(fasta_path: &str, d: &Vec<(String, String)>) {
 }
 
 pub fn write_fai(path: &str) {
-    let mut faidx = Command::new("samtools").arg("faidx").arg(path).spawn().expect("Samtools faidx failed to start");
+    let mut faidx = Command::new("samtools")
+        .arg("faidx")
+        .arg(path)
+        .spawn()
+        .expect("Samtools faidx failed to start");
     faidx.wait().unwrap();
 }
 
@@ -536,8 +574,6 @@ pub fn create_bam(ref_path: &str, reads_path: &str, bam_path: &str) -> Result<()
     Ok(())
 }
 
-
-
 #[cfg(test)]
 mod tests {
     use super::*;