fix: cases of empty sequence (#61)

varfish-org · Mar 27, 2023 · 0a6a109 · 0a6a109
1 parent 54231b9
commit 0a6a109
Show file tree

Hide file tree

Showing 2 changed files with 16 additions and 6 deletions.
diff --git a/src/mapper/altseq.rs b/src/mapper/altseq.rs
@@ -782,7 +782,11 @@ impl AltSeqToHgvsp {
             aa_end = aa_start.clone();
 
             reference = "".to_owned();
-            alternative = insertion.chars().next().unwrap().to_string();
+            alternative = insertion
+                .chars()
+                .next()
+                .map(|c| c.to_string())
+                .unwrap_or_default();
             is_ext = true;
         } else if *is_frameshift {
             // frameshift
@@ -793,7 +797,11 @@ impl AltSeqToHgvsp {
             aa_end = aa_start.clone();
 
             reference = "".to_owned();
-            alternative = insertion.chars().next().unwrap().to_string();
+            alternative = insertion
+                .chars()
+                .next()
+                .map(|c| c.to_string())
+                .unwrap_or_default();
 
             fsext_len = insertion
                 .find('*')

diff --git a/src/sequences.rs b/src/sequences.rs
@@ -541,12 +541,14 @@ pub fn aa_to_aa3(seq: &str) -> Result<String, anyhow::Error> {
 #[allow(dead_code)]
 pub fn aa1_to_aa3(seq: &str) -> Result<String, anyhow::Error> {
     let mut result = String::new();
+    if seq.is_empty() {
+        return Ok(result);
+    }
 
     for i in 0..seq.len() {
-        let aa3 = AA1_TO_AA3_LUT.get(&seq[i..(i + 1)]).ok_or(anyhow::anyhow!(
-            "Invalid 1-letter amino acid: {}",
-            &seq[i..(i + 1)]
-        ))?;
+        let aa3 = AA1_TO_AA3_LUT
+            .get(&seq[i..(i + 1)])
+            .ok_or_else(|| anyhow::anyhow!("Invalid 1-letter amino acid: {}", &seq[i..(i + 1)]))?;
         result.push_str(aa3);
     }