changes

src/lib.rs

@@ -5,7 +5,7 @@ use noodles_fasta as fasta;
 use rust_htslib::bam::{self, Record};
 use std::{
     collections::{HashMap, VecDeque},
-    fmt,
+    fmt::{self, format},
     fs::{self, File},
     io::{BufWriter, Write},
     process::{Command, Stdio},
@@ -345,6 +345,18 @@ impl Contig {
         let bam_path = format!("{contig_dir}/{}.bam", self.id);
         create_bam(&fasta_path, &reads_path, &bam_path)?;
 
+        let bed_path = format!("{contig_dir}/contig.bed");
+        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))
+                ];
+                write_bed(&bed_path, &d)?;
+            },
+            _ => ()
+        }
+
         Ok(())
     }
 
@@ -422,6 +434,16 @@ fn group_mappings(mappings: &mut Vec<Mapping>) -> Result<Vec<Vec<Mapping>>> {
     Ok(alignments)
 }
 
+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"));
+        writer.write_all(row.as_bytes())?;
+    }
+    Ok(())
+}
+
 // unique
 pub fn write_fastq(fastq_path: &str, d: &Vec<Record>) -> Result<()> {
     let file = File::create(fastq_path)?;
@@ -438,7 +460,6 @@ pub fn write_fastq(fastq_path: &str, d: &Vec<Record>) -> Result<()> {
     Ok(())
 }
 
-// unique
 pub fn write_fasta(fasta_path: &str, d: &Vec<(String, String)>) {
     let file = File::create(fasta_path).unwrap();
     let mut writer = fasta::writer::Builder::default().build_with_writer(file);