fix: fixing projection issues with cdot::json::Provider

src/data/uta_sr.rs

@@ -229,7 +229,7 @@ pub mod test_helpers {
     }
 
     /// Helper that builds the cache writing SeqRepo with inner stock SeqRepo.
-    fn build_writing_sr(
+    pub fn build_writing_sr(
         sr_cache_path: String,
     ) -> Result<(Rc<dyn SeqRepoInterface>, String), anyhow::Error> {
         let seqrepo_path = std::env::var("TEST_SEQREPO_PATH")

src/mapper/alignment.rs

@@ -198,7 +198,8 @@ impl Mapper {
                     ));
                 }
 
-                let cigar_mapper = CigarMapper::new(&build_tx_cigar(&tx_exons, strand)?);
+                let cigar = build_tx_cigar(&tx_exons, strand)?;
+                let cigar_mapper = CigarMapper::new(&cigar);
                 let tgt_len = cigar_mapper.tgt_len;
 
                 (

src/mapper/assembly.rs

@@ -105,7 +105,6 @@ impl Mapper {
             .get_assembly_map(config.assembly)
             .keys()
             .clone()
-            .into_iter()
             .map(|s| s.to_string())
             .collect::<HashSet<_>>();
         let asm_map = HashMap::from_iter(
@@ -262,7 +261,7 @@ impl Mapper {
                     .map(|rec| rec.tx_ac)
                     .collect::<Vec<_>>())
             }
-            _ => return Err(anyhow::anyhow!("Not a GenomeVariant: {}", &var_g)),
+            _ => Err(anyhow::anyhow!("Not a GenomeVariant: {}", &var_g)),
         }
     }
 

src/mapper/variant.rs

@@ -153,9 +153,9 @@ impl Mapper {
         self.validator.validate(var_g)?;
         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)
+            self.g_to_c(var_g, tx_ac, alt_aln_method)
         } else {
-            self.g_to_n(&var_g, tx_ac, alt_aln_method)
+            self.g_to_n(var_g, tx_ac, alt_aln_method)
         }
     }
 
@@ -580,12 +580,10 @@ impl Mapper {
         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
-                ))
-            }
+            _ => Err(anyhow::anyhow!(
+                "Expected transcript or CDS variant but received {}",
+                &var_t
+            )),
         }
     }
 

src/parser/impl_parse.rs

@@ -927,15 +927,10 @@ mod test {
             let inputs = if in_type == "list" {
                 in_string
                     .split('|')
-                    .into_iter()
                     .map(|s| s.to_string())
                     .collect::<Vec<_>>()
             } else if in_type == "string" {
-                in_string
-                    .chars()
-                    .into_iter()
-                    .map(|c| c.to_string())
-                    .collect::<Vec<_>>()
+                in_string.chars().map(|c| c.to_string()).collect::<Vec<_>>()
             } else if in_type == "one" {
                 vec![in_string.to_string()]
             } else {