fix: variant mapper g_to_t used wrong logic (#32)

src/mapper/variant.rs

@@ -133,21 +133,17 @@ impl Mapper {
     /// * `alt_al_method` -- alignment method, e.g., `splign`
     pub fn g_to_t(
         &self,
-        var_t: &HgvsVariant,
-        alt_ac: &str,
+        var_g: &HgvsVariant,
+        tx_ac: &str,
         alt_aln_method: &str,
     ) -> Result<HgvsVariant, anyhow::Error> {
-        self.validator.validate(var_t)?;
-        let var_t = self.replace_reference(var_t.clone())?;
-        match var_t {
-            HgvsVariant::TxVariant { .. } => self.n_to_g(&var_t, alt_ac, alt_aln_method),
-            HgvsVariant::CdsVariant { .. } => self.c_to_g(&var_t, alt_ac, alt_aln_method),
-            _ => {
-                return Err(anyhow::anyhow!(
-                    "Expected transcript or CDS variant but received {}",
-                    &var_t
-                ))
-            }
+        self.validator.validate(var_g)?;
+        let var_g = self.replace_reference(var_g.clone())?;
+        let mapper = self.build_alignment_mapper(tx_ac, var_g.accession(), alt_aln_method)?;
+        if mapper.is_coding_transcript() {
+            self.g_to_c(&var_g, tx_ac, alt_aln_method)
+        } else {
+            self.g_to_n(&var_g, tx_ac, alt_aln_method)
         }
     }
 

tests/data/data/bootstrap.sh

@@ -28,16 +28,12 @@ psql-uta()
 
 pg-list()
 {
-    result=""
-    while [[ $# -ne 0 ]]; do
-        if [[ ! -z "${result}" ]]; then
-            result="${result}, "
-        fi
-        result="${result}'$1'"
-        shift
-    done
-    result="(${result})"
-    echo $result
+    echo $* \
+    | tr ' ' '\n' \
+    | sed -e "s/^/'/g" -e "s/$/'/g" \
+    | tr '\n' ',' \
+    | sed -e 's/,$//g' \
+    | sed -e "s/^/(/g" -e "s/$/)/g"
 }
 
 # Initialization ------------------------------------------------------------