vcf bnd

src/variant/variant.rs

@@ -280,46 +280,101 @@ impl VcfVariant {
     pub fn bnd_desc(&self) -> anyhow::Result<BNDDesc> {
         let alt = self.alternative.to_string();
         if alt.contains('[') || alt.contains(']') {
-            let b_sens = alt.contains('[');
-
-            let a_sens = if b_sens {
-                !alt.starts_with('[')
+            let extending_right = alt.contains('[');
+            let alt_rep = alt.replace("[", ";").replace("]", ";");
+            let alt_is_joined_after = !alt_rep.starts_with(";");
+            let parts = alt_rep
+                .split(";")
+                .filter(|c| !c.is_empty())
+                .collect::<Vec<&str>>();
+
+            if alt_is_joined_after {
+                // a is ref b is alt
+                let a_sens = true;
+                let a_contig = self.position.contig();
+                let a_position = self.position.position + 1;
+
+                let added_nt = parts[0][1..].to_string();
+
+                let b_sens = alt.contains('[');
+                let (contig, pos) = parts[1].split_once(':').unwrap();
+                let b_contig = contig.to_string();
+                let b_position: u32 = pos.parse()?;
+
+                Ok(BNDDesc {
+                    a_contig,
+                    a_position,
+                    a_sens,
+                    b_contig,
+                    b_position,
+                    b_sens,
+                    added_nt,
+                })
             } else {
-                !alt.starts_with(']')
-            };
-
-            let parts: Vec<&str> = alt
-                .split(&['[', ']', ':'])
-                .filter(|v| !v.is_empty())
-                .collect();
-
-            if parts.len() != 3 {
-                return Err(anyhow::anyhow!("Failed to parse parts: {parts:?}"));
+                // a is alt b is ref
+                let b_sens = true;
+                let b_contig = self.position.contig();
+                let b_position = self.position.position + 1;
+
+                let mut added_nt = parts[1].to_string();
+                added_nt.pop();
+
+                let a_sens = alt.contains(']');
+                let (contig, pos) = parts[0].split_once(':').unwrap();
+                let a_contig = contig.to_string();
+                let a_position: u32 = pos.parse()?;
+
+                Ok(BNDDesc {
+                    a_contig,
+                    a_position,
+                    a_sens,
+                    b_contig,
+                    b_position,
+                    b_sens,
+                    added_nt,
+                })
             }
 
-            let (nt, b_contig, b_position) = if a_sens {
-                (parts[0], parts[1], parts[2])
-            } else {
-                (parts[2], parts[0], parts[1])
-            };
-
-            let added_nt = if nt.len() > 1 {
-                nt[1..].to_string()
-            } else {
-                nt.to_string()
-            };
-
-            Ok(BNDDesc {
-                a_contig: self.position.contig(),
-                a_position: self.position.position + 1,
-                a_sens,
-                b_contig: b_contig.to_string(),
-                b_position: b_position
-                    .parse()
-                    .map_err(|e| anyhow::anyhow!("Failed to parse: {b_position}\n{e}"))?,
-                b_sens,
-                added_nt,
-            })
+            // let b_sens = alt.contains('[');
+            //
+            // let a_sens = if b_sens {
+            //     !alt.starts_with('[')
+            // } else {
+            //     !alt.starts_with(']')
+            // };
+            //
+            // let parts: Vec<&str> = alt
+            //     .split(&['[', ']', ':'])
+            //     .filter(|v| !v.is_empty())
+            //     .collect();
+            //
+            // if parts.len() != 3 {
+            //     return Err(anyhow::anyhow!("Failed to parse parts: {parts:?}"));
+            // }
+            //
+            // let (nt, b_contig, b_position) = if a_sens {
+            //     (parts[0], parts[1], parts[2])
+            // } else {
+            //     (parts[2], parts[0], parts[1])
+            // };
+            //
+            // let added_nt = if nt.len() > 1 {
+            //     nt[1..].to_string()
+            // } else {
+            //     nt.to_string()
+            // };
+            //
+            // Ok(BNDDesc {
+            //     a_contig: self.position.contig(),
+            //     a_position: self.position.position + 1,
+            //     a_sens,
+            //     b_contig: b_contig.to_string(),
+            //     b_position: b_position
+            //         .parse()
+            //         .map_err(|e| anyhow::anyhow!("Failed to parse: {b_position}\n{e}"))?,
+            //     b_sens,
+            //     added_nt,
+            // })
         } else {
             Err(anyhow::anyhow!("The alteration is not BND: {alt}"))
         }