chore: fix some clippy lints (#184)

varfish-org · Jul 8, 2024 · 1e9b0aa · 1e9b0aa
1 parent 4345377
commit 1e9b0aa
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Showing 3 changed files with 18 additions and 24 deletions.
diff --git a/src/data/cdot/json.rs b/src/data/cdot/json.rs
@@ -39,7 +39,7 @@ pub struct Config {
 /// The method are not implemented.
 ///
 /// The method `get_tx_exons()` returns `None` for record entries `tx_aseq`, and `alt_aseq`
-/// and `std::i32::MAX` for `tx_exon-set_id`, `alt_exon_set_id`, `tx_exon_id`, `alt_exon_id`,
+/// and `i32::MAX` for `tx_exon-set_id`, `alt_exon_set_id`, `tx_exon_id`, `alt_exon_id`,
 /// `exon_aln_id`.
 pub struct Provider {
     inner: TxProvider,
@@ -853,11 +853,11 @@ impl TxProvider {
                     cigar: exon.cigar.clone(),
                     tx_aseq: None,
                     alt_aseq: None,
-                    tx_exon_set_id: std::i32::MAX,
-                    alt_exon_set_id: std::i32::MAX,
-                    tx_exon_id: std::i32::MAX,
-                    alt_exon_id: std::i32::MAX,
-                    exon_aln_id: std::i32::MAX,
+                    tx_exon_set_id: i32::MAX,
+                    alt_exon_set_id: i32::MAX,
+                    tx_exon_id: i32::MAX,
+                    alt_exon_id: i32::MAX,
+                    exon_aln_id: i32::MAX,
                 })
                 .collect())
         } else {

diff --git a/src/normalizer.rs b/src/normalizer.rs
@@ -299,11 +299,11 @@ impl<'a> Normalizer<'a> {
                     .last()
                     .expect("should not happen; must have at least one exon"),
             );
-            exon_ends.push(std::i32::MAX);
+            exon_ends.push(i32::MAX);
 
             // Find the end pos of the exon where the var locates.
             let _left = 0;
-            let _right = std::i32::MAX;
+            let _right = i32::MAX;
 
             // NB: the following content is from the original Python code.
             // TODO: #242: implement methods to find tx regions
@@ -357,7 +357,7 @@ impl<'a> Normalizer<'a> {
             Ok(left..right)
         } else {
             // For variant types g., m., etc.
-            Ok(0..std::i32::MAX)
+            Ok(0..i32::MAX)
         }
     }
 
@@ -846,7 +846,7 @@ impl<'a> Normalizer<'a> {
                 var,
                 HgvsVariant::GenomeVariant { .. } | HgvsVariant::MtVariant { .. }
             ) {
-                std::i32::MAX
+                i32::MAX
             } else {
                 let id_info = self.provider.get_tx_identity_info(var.accession())?;
                 id_info.lengths.into_iter().sum()

diff --git a/src/parser/ds.rs b/src/parser/ds.rs
@@ -483,20 +483,14 @@ impl HgvsVariant {
                 .try_into()
                 .ok()
                 .map(|l| Mu::from(l, loc_edit.loc.is_certain())),
-            HgvsVariant::TxVariant { loc_edit, .. } => loc_edit
-                .loc
-                .inner()
-                .clone()
-                .try_into()
-                .ok()
-                .map(|l| Mu::from(l, loc_edit.loc.is_certain())),
-            HgvsVariant::RnaVariant { loc_edit, .. } => loc_edit
-                .loc
-                .inner()
-                .clone()
-                .try_into()
-                .ok()
-                .map(|l| Mu::from(l, loc_edit.loc.is_certain())),
+            HgvsVariant::TxVariant { loc_edit, .. } => {
+                Some(From::from(loc_edit.loc.inner().clone()))
+                    .map(|l| Mu::from(l, loc_edit.loc.is_certain()))
+            }
+            HgvsVariant::RnaVariant { loc_edit, .. } => {
+                Some(From::from(loc_edit.loc.inner().clone()))
+                    .map(|l| Mu::from(l, loc_edit.loc.is_certain()))
+            }
             HgvsVariant::ProtVariant {
                 loc_edit: ProtLocEdit::Ordinary { loc, .. },
                 ..