From 2db5e92316930e76d4b58d47ccc1d2ba2c1010fe Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Wed, 22 Mar 2023 11:50:34 +0100
Subject: [PATCH] feat: improved normalizer configuration (#52)

---
 src/mapper/variant.rs |  7 +++++--
 src/normalizer.rs     | 18 ++++++++++++------
 2 files changed, 17 insertions(+), 8 deletions(-)

diff --git a/src/mapper/variant.rs b/src/mapper/variant.rs
index b144a74..bfd4cb5 100644
--- a/src/mapper/variant.rs
+++ b/src/mapper/variant.rs
@@ -7,7 +7,7 @@ use log::{debug, info};
 use super::alignment::{Config as AlignmentConfig, Mapper as AlignmentMapper};
 use crate::{
     data::interface::Provider,
-    normalizer::{self, Normalizer},
+    normalizer::{self, Config as NormalizerConfig, Normalizer},
     parser::{
         Accession, CdsInterval, CdsLocEdit, CdsPos, GeneSymbol, GenomeInterval, GenomeLocEdit,
         HgvsVariant, Mu, NaEdit, TxInterval, TxLocEdit, TxPos,
@@ -130,7 +130,10 @@ impl Mapper {
             self,
             self.provider.clone(),
             self.validator.clone(),
-            Default::default(),
+            NormalizerConfig {
+                replace_reference: self.config.replace_reference,
+                ..Default::default()
+            },
         ))
     }
 
diff --git a/src/normalizer.rs b/src/normalizer.rs
index a27b1f9..668967a 100644
--- a/src/normalizer.rs
+++ b/src/normalizer.rs
@@ -23,13 +23,14 @@ pub enum Direction {
 /// Configuration for the normalizer.
 #[derive(Debug, Clone)]
 pub struct Config {
-    alt_aln_method: String,
-    cross_boundaries: bool,
-    shuffle_direction: Direction,
+    pub alt_aln_method: String,
+    pub cross_boundaries: bool,
+    pub shuffle_direction: Direction,
+    pub replace_reference: bool,
     // TODO: inconsistent with passing in the validator...
     #[allow(dead_code)]
-    validate: bool,
-    window_size: usize,
+    pub validate: bool,
+    pub window_size: usize,
 }
 
 impl Default for Config {
@@ -38,6 +39,7 @@ impl Default for Config {
             alt_aln_method: "splign".to_string(),
             cross_boundaries: false,
             shuffle_direction: Direction::FiveToThree,
+            replace_reference: true,
             validate: true,
             window_size: 20,
         }
@@ -125,7 +127,11 @@ impl<'a> Normalizer<'a> {
 
         // NB: once we support gene conversions, guard against this here as well.
 
-        let var = self.mapper.replace_reference(var)?;
+        let var = if self.config.replace_reference {
+            self.mapper.replace_reference(var)?
+        } else {
+            var
+        };
 
         // Guard against identity variants.
         if let Some(na_edit) = var.na_edit() {