begining of hgvs todo add insertion and cytobands

src/lib.rs

@@ -79,13 +79,15 @@ impl ContigRef {
                     let chr = a.target_name.clone().unwrap_or("UNKNOWN".to_string());
                     let del_start = a.target_end;
                     let del_end = b.target_start;
-                    Some(format!("{chr}:{del_start}_{del_end}"))
+                    let hgvs = format!("{chr}:{del_start}_{del_end}");
+                    Some(hgvs)
                 } else {
                     let a_chr = a.target_name.clone().unwrap_or("UNKNOWN".to_string());
                     let a_bp = a.target_end;
                     let b_chr = b.target_name.clone().unwrap_or("UNKNOWN".to_string());
                     let b_bp = b.target_end;
-                    Some(format!("{a_chr}:{a_bp}delins[{b_chr}:{b_bp}]"))
+                    let hgvs = format!("{a_chr}:{a_bp}delins[{b_chr}:{b_bp}]");
+                    Some(hgvs)
                 }
             }
             ContigRef::ChimericMultiple(_) => None,
@@ -330,7 +332,12 @@ impl Contig {
     }
 
     pub fn to_igv(&self, dir_path: &str) -> Result<()> {
-        let contig_dir = format!("{dir_path}/{}", self.id);
+        let contig_name = if let Some(hgvs) = self.hgvs() {
+            hgvs
+        } else {
+            self.id.clone()
+        };
+        let contig_dir = format!("{dir_path}/{contig_name}");
         fs::create_dir_all(contig_dir.clone())?;
 
         let fasta_path = format!("{contig_dir}/contig.fa");
@@ -352,7 +359,7 @@ impl Contig {
         write_fasta(&reads_path, &n_reads);
 
         let bam_path = format!("{contig_dir}/{}.bam", self.id);
-        create_bam(&fasta_path, &reads_path, &bam_path)?;
+        write_bam(&fasta_path, &reads_path, &bam_path)?;
 
         let bed_path = format!("{contig_dir}/contig.bed");
         match &self.contig_ref {
@@ -528,9 +535,7 @@ pub fn write_fai(path: &str) {
     faidx.wait().unwrap();
 }
 
-// pub fn write_aln_sh()
-
-pub fn create_bam(ref_path: &str, reads_path: &str, bam_path: &str) -> Result<()> {
+pub fn write_bam(ref_path: &str, reads_path: &str, bam_path: &str) -> Result<()> {
     let rg_id = uuid::Uuid::new_v4();
 
     let mm2 = Command::new("minimap2")