From 761d416e9180d35aeb5655ca257a6f2d562ff64a Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Tue, 6 Feb 2024 09:55:01 +0100
Subject: [PATCH] feat: fix parsing of non-uppercase SvType (bihealth/reev#434)
 (#95)

---
 src/lib/genomicVars.spec.ts |  4 ++--
 src/lib/genomicVars.ts      | 14 ++++++++++++--
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/src/lib/genomicVars.spec.ts b/src/lib/genomicVars.spec.ts
index b2460f4..0c8a5e3 100644
--- a/src/lib/genomicVars.spec.ts
+++ b/src/lib/genomicVars.spec.ts
@@ -458,8 +458,8 @@ describe.concurrent('parseSeparatedStrucvar()', () => {
     })
   })
 
-  it('parse DEL:GRCh37:1:100:200', () => {
-    expect(parseSeparatedStrucvar('DEL:1:100:200')).toEqual({
+  it('parse Del:GRCh37:1:100:200', () => {
+    expect(parseSeparatedStrucvar('Del:1:100:200')).toEqual({
       chrom: '1',
       copyNumber: undefined,
       genomeBuild: 'grch37',
diff --git a/src/lib/genomicVars.ts b/src/lib/genomicVars.ts
index 7bdc6a6..7e1d9cd 100644
--- a/src/lib/genomicVars.ts
+++ b/src/lib/genomicVars.ts
@@ -67,7 +67,7 @@ export type SvType = 'DEL' | 'DUP'
 
 /** Interface for regex groups when parsing with `REGEX_CNV_COLON` or `REGEX_CNV_HYPHEN`. */
 export interface RegexCnvGroups {
-  svType: SvType
+  svType: string
   genomeBuild?: string
   chrom?: string
   sequence?: string
@@ -420,7 +420,7 @@ export function parseSeparatedStrucvar(
   // Obtain the genome build and chromosome from the parsed groups.  Also,
   // perform validation.
   const {
-    svType,
+    svType: svType$Regex,
     genomeBuild: genomeBuildValue,
     sequence,
     chrom: chromValue,
@@ -460,6 +460,16 @@ export function parseSeparatedStrucvar(
     }
   }
 
+  // Normalize the SV type.
+  let svType: SvType
+  if (svType$Regex.toUpperCase() === 'DEL') {
+    svType = 'DEL'
+  } else if (svType$Regex.toUpperCase() === 'DUP') {
+    svType = 'DUP'
+  } else {
+    throw new ParseError(`Unknown SV type: ${svType$Regex}`)
+  }
+
   return {
     svType,
     genomeBuild,