fix: problem with annotating stop_retained insertions (#131) (#132)

Cargo.toml

@@ -31,13 +31,14 @@ seqrepo = { version = "0.8", features = ["cached"] }
 serde_json = "1.0"
 serde = { version = "1.0", features = ["derive"] }
 thiserror = "1.0"
-indexmap = { version = "2.0.0", features = ["serde"] }
+indexmap = { version = "2", features = ["serde"] }
 
 [dev-dependencies]
 anyhow = "1.0"
 criterion = "0.5"
 csv = "1.2"
 env_logger = "0.10"
+insta = { version = "1", features = ["yaml"] }
 pretty_assertions = "1.3"
 rstest = "0.18"
 test-log = "0.2"

src/mapper/altseq.rs

@@ -88,6 +88,7 @@ impl RefTranscriptData {
     }
 }
 
+#[derive(Debug, Clone)]
 pub struct AltTranscriptData {
     /// Transcript nucleotide sequence.
     #[allow(dead_code)]
@@ -697,10 +698,14 @@ impl AltSeqToHgvsp {
                             .last()
                             .expect("should not happen; checked for being non-empty above")
                             + 1;
-                        (
-                            format!("{}{}", deletion, &ref_sub[..max_diff]),
-                            format!("{}{}", insertion, &alt_sub[..max_diff]),
-                        )
+                        if max_diff > ref_sub.len() || max_diff > alt_sub.len() {
+                            (deletion.clone(), insertion.clone())
+                        } else {
+                            (
+                                format!("{}{}", deletion, &ref_sub[..max_diff]),
+                                format!("{}{}", insertion, &alt_sub[..max_diff]),
+                            )
+                        }
                     } else {
                         (deletion, insertion)
                     };

src/mapper/snapshots/hgvs__mapper__variant__test__issue_131.snap

@@ -0,0 +1,10 @@
+---
+source: src/mapper/variant.rs
+expression: "&var_p_test"
+---
+ProtVariant:
+  accession:
+    value: NP_001240838.1
+  gene_symbol: ~
+  loc_edit: NoChange
+

src/mapper/variant.rs

@@ -959,6 +959,19 @@ mod test {
 
     use super::{Config, Mapper};
 
+    #[test]
+    fn issue_131() -> Result<(), Error> {
+        let mapper = build_mapper()?;
+
+        let var_c = HgvsVariant::from_str("NM_001253909.2:c.416_417insGTG")?;
+        let var_p_test = mapper.c_to_p(&var_c, None)?;
+
+        assert_eq!(format!("{}", &var_p_test), "NP_001240838.1:p.=");
+        insta::assert_yaml_snapshot!(&var_p_test);
+
+        Ok(())
+    }
+
     #[test]
     fn test_sync() {
         fn is_sync<T: Sync>() {}

src/parser/ds.rs

@@ -6,7 +6,7 @@ use crate::parser::error::Error;
 use log::warn;
 
 /// Expression of "maybe uncertain".
-#[derive(Clone, Debug, PartialEq)]
+#[derive(Clone, Debug, PartialEq, serde::Serialize, serde::Deserialize)]
 pub enum Mu<T> {
     /// Certain variant of `T`.
     Certain(T),
@@ -53,7 +53,7 @@ impl<T> Mu<T> {
 }
 
 /// Representation of gene symbol, e.g., `TTN` or `Ttn`.
-#[derive(Clone, Debug, PartialEq)]
+#[derive(Clone, Debug, PartialEq, serde::Serialize, serde::Deserialize)]
 pub struct GeneSymbol {
     pub value: String,
 }
@@ -79,7 +79,7 @@ impl Deref for GeneSymbol {
 }
 
 /// Edit of nucleic acids.
-#[derive(Clone, Debug, PartialEq)]
+#[derive(Clone, Debug, PartialEq, serde::Serialize, serde::Deserialize)]
 pub enum NaEdit {
     /// A substitution where both reference and alternative allele are nucleic acid strings
     /// (or empty).
@@ -189,7 +189,7 @@ impl NaEdit {
 }
 
 /// Uncertain change through extension.
-#[derive(Clone, Debug, PartialEq, Default)]
+#[derive(Clone, Debug, PartialEq, Default, serde::Serialize, serde::Deserialize)]
 pub enum UncertainLengthChange {
     #[default]
     None,
@@ -198,7 +198,7 @@ pub enum UncertainLengthChange {
 }
 
 /// Representation of accession, e.g., `NM_01234.5`.
-#[derive(Clone, Debug, PartialEq)]
+#[derive(Clone, Debug, PartialEq, serde::Serialize, serde::Deserialize)]
 pub struct Accession {
     pub value: String,
 }
@@ -224,7 +224,7 @@ impl Accession {
 }
 
 /// Protein edit with interval end edit.
-#[derive(Clone, Debug, PartialEq)]
+#[derive(Clone, Debug, PartialEq, serde::Serialize, serde::Deserialize)]
 pub enum ProteinEdit {
     Fs {
         alternative: Option<String>,
@@ -259,7 +259,7 @@ pub enum ProteinEdit {
 }
 
 /// A HGVS variant specification.
-#[derive(Clone, Debug, PartialEq)]
+#[derive(Clone, Debug, PartialEq, serde::Serialize, serde::Deserialize)]
 pub enum HgvsVariant {
     /// Variant specification with `c.` location.
     CdsVariant {
@@ -563,7 +563,7 @@ impl HgvsVariant {
 }
 
 /// Coding sequence location with edit.
-#[derive(Clone, Debug, PartialEq)]
+#[derive(Clone, Debug, PartialEq, serde::Serialize, serde::Deserialize)]
 pub struct CdsLocEdit {
     /// Location on the CDS.
     pub loc: Mu<CdsInterval>,
@@ -596,7 +596,7 @@ impl CdsLocEdit {
 }
 
 /// CDS position interval.
-#[derive(Clone, Debug, PartialEq)]
+#[derive(Clone, Debug, PartialEq, serde::Serialize, serde::Deserialize)]
 pub struct CdsInterval {
     /// Start position
     pub start: CdsPos,
@@ -627,14 +627,14 @@ impl TryFrom<CdsInterval> for Range<i32> {
 
 /// Specifies whether the CDS position is relative to the CDS start or
 /// CDS end.
-#[derive(Clone, Copy, Debug, PartialEq)]
+#[derive(Clone, Copy, Debug, PartialEq, serde::Serialize, serde::Deserialize)]
 pub enum CdsFrom {
     Start,
     End,
 }
 
 /// CDS position.
-#[derive(Clone, Debug, PartialEq)]
+#[derive(Clone, Debug, PartialEq, serde::Serialize, serde::Deserialize)]
 pub struct CdsPos {
     /// Base position.
     pub base: i32,
@@ -645,7 +645,7 @@ pub struct CdsPos {
 }
 
 /// Genome sequence location with edit.
-#[derive(Clone, Debug, PartialEq)]
+#[derive(Clone, Debug, PartialEq, serde::Serialize, serde::Deserialize)]
 pub struct GenomeLocEdit {
     /// Location on the genome.
     pub loc: Mu<GenomeInterval>,
@@ -678,7 +678,7 @@ impl GenomeLocEdit {
 }
 
 /// Genome position interval.
-#[derive(Clone, Debug, PartialEq)]
+#[derive(Clone, Debug, PartialEq, serde::Serialize, serde::Deserialize)]
 pub struct GenomeInterval {
     /// Start position
     pub start: Option<i32>,
@@ -701,7 +701,7 @@ impl TryInto<Range<i32>> for GenomeInterval {
 }
 
 /// Mitochondrial sequence location with edit.
-#[derive(Clone, Debug, PartialEq)]
+#[derive(Clone, Debug, PartialEq, serde::Serialize, serde::Deserialize)]
 pub struct MtLocEdit {
     /// Location on the mitochondrium.
     pub loc: Mu<MtInterval>,
@@ -733,7 +733,7 @@ impl MtLocEdit {
     }
 }
 /// Mitochondrial position interval.
-#[derive(Clone, Debug, PartialEq)]
+#[derive(Clone, Debug, PartialEq, serde::Serialize, serde::Deserialize)]
 pub struct MtInterval {
     /// Start position
     pub start: Option<i32>,
@@ -756,7 +756,7 @@ impl TryInto<Range<i32>> for MtInterval {
 }
 
 /// Transcript sequence location with edit.
-#[derive(Clone, Debug, PartialEq)]
+#[derive(Clone, Debug, PartialEq, serde::Serialize, serde::Deserialize)]
 pub struct TxLocEdit {
     /// Loction on a transcript.
     pub loc: Mu<TxInterval>,
@@ -789,7 +789,7 @@ impl TxLocEdit {
 }
 
 /// Transcript position interval.
-#[derive(Clone, Debug, PartialEq)]
+#[derive(Clone, Debug, PartialEq, serde::Serialize, serde::Deserialize)]
 pub struct TxInterval {
     /// Start position
     pub start: TxPos,
@@ -813,7 +813,7 @@ impl From<TxInterval> for Range<i32> {
 }
 
 /// Transcript position.
-#[derive(Clone, Debug, PartialEq)]
+#[derive(Clone, Debug, PartialEq, serde::Serialize, serde::Deserialize)]
 pub struct TxPos {
     /// Base position.
     pub base: i32,
@@ -822,7 +822,7 @@ pub struct TxPos {
 }
 
 /// RNA sequence location with edit.
-#[derive(Clone, Debug, PartialEq)]
+#[derive(Clone, Debug, PartialEq, serde::Serialize, serde::Deserialize)]
 pub struct RnaLocEdit {
     /// Location on a transcript.
     pub loc: Mu<RnaInterval>,
@@ -854,7 +854,7 @@ impl RnaLocEdit {
     }
 }
 /// RNA position interval.
-#[derive(Clone, Debug, PartialEq)]
+#[derive(Clone, Debug, PartialEq, serde::Serialize, serde::Deserialize)]
 pub struct RnaInterval {
     /// Start position
     pub start: RnaPos,
@@ -878,7 +878,7 @@ impl From<RnaInterval> for Range<i32> {
 }
 
 /// RNA position.
-#[derive(Clone, Debug, PartialEq)]
+#[derive(Clone, Debug, PartialEq, serde::Serialize, serde::Deserialize)]
 pub struct RnaPos {
     /// Base position.
     pub base: i32,
@@ -887,7 +887,7 @@ pub struct RnaPos {
 }
 
 /// Protein sequence location with edit or special.
-#[derive(Clone, Debug, PartialEq)]
+#[derive(Clone, Debug, PartialEq, serde::Serialize, serde::Deserialize)]
 pub enum ProtLocEdit {
     Ordinary {
         loc: Mu<ProtInterval>,
@@ -908,7 +908,7 @@ pub enum ProtLocEdit {
 }
 
 /// Protein position interval.
-#[derive(Clone, Debug, PartialEq)]
+#[derive(Clone, Debug, PartialEq, serde::Serialize, serde::Deserialize)]
 pub struct ProtInterval {
     /// Start position
     pub start: ProtPos,
@@ -927,7 +927,7 @@ impl From<ProtInterval> for Range<i32> {
 }
 
 /// Protein position.
-#[derive(Clone, Debug, PartialEq, Default)]
+#[derive(Clone, Debug, PartialEq, Default, serde::Serialize, serde::Deserialize)]
 pub struct ProtPos {
     /// Amino acid value.
     pub aa: String,
@@ -973,13 +973,13 @@ mod test {
         assert_eq!(Mu::from(Some(1), false), Mu::Uncertain(Some(1)));
     }
 
-    #[derive(Clone, Debug, PartialEq)]
+    #[derive(Clone, Debug, PartialEq, serde::Serialize, serde::Deserialize)]
     pub struct TestInterval {
         pub start: TestPos,
         pub end: TestPos,
     }
 
-    #[derive(Clone, Debug, PartialEq)]
+    #[derive(Clone, Debug, PartialEq, serde::Serialize, serde::Deserialize)]
     pub struct TestPos {
         pub base: i32,
         pub offset: Option<i32>,

tests/data/data/bootstrap.sh

@@ -67,6 +67,7 @@ ADGRL3
 ADRA2B
 ADRB2
 AGBL5
+AKR1C3
 ALG9
 AOAH
 ASB18