Use CDSpos instead of cDNApos

ccmbioinfo · Jan 14, 2025 · e76e161 · e76e161
1 parent e2ffc77
commit e76e161
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Showing 3 changed files with 7 additions and 5 deletions.
diff --git a/server/src/resolvers/getVariantsResolver/utils/annotateCadd.ts b/server/src/resolvers/getVariantsResolver/utils/annotateCadd.ts
@@ -28,7 +28,7 @@ const annotate = timeit('annotateCadd')(
 
       if (key in annotationKeys) {
         /* eslint-disable-next-line @typescript-eslint/no-unused-vars */
-        const { aaAlt, aaPos, aaRef, cdnaPos, chrom, pos, alt, ref, ...rest } = annotationKeys[key];
+        const { aaAlt, aaPos, aaRef, cdsPos, chrom, pos, alt, ref, ...rest } = annotationKeys[key];
         response.variant.info = {
           ...response.variant.info,
           aaChange:
@@ -42,7 +42,8 @@ const annotate = timeit('annotateCadd')(
                   aaAlt === aaRef ? '=' : AMINO_ACID_MAPPING[aaAlt]
                 }`
               : 'NA',
-          cdna: alt && cdnaPos && cdnaPos !== 'NA' && ref ? `c.${cdnaPos}${ref}>${alt}` : 'NA',
+          // uses CDSpos instead of cDNApos
+          cdna: alt && cdsPos && cdsPos !== 'NA' && ref ? `c.${cdsPos}${ref}>${alt}` : 'NA',
           ...rest,
         };
       }

diff --git a/server/src/resolvers/getVariantsResolver/utils/fetchCaddAnnotations.ts b/server/src/resolvers/getVariantsResolver/utils/fetchCaddAnnotations.ts
@@ -69,7 +69,8 @@ const _getAnnotations = async (position: string, assemblyId: string) => {
     oAA: 17
     nAA: 18
     FeatureID: 20
-    cDNApos: 25
+    cDNApos: 25  // deprecated for use in OSMP
+    CDSpos: 27  // replaces cDNApos
     protpos: 29
     spliceAI-acc-gain: 94 (GRCh37) 109 (GRCh38)
     spliceAI-acc-loss: 95 (GRCh37) 110 (GRCh38)
@@ -95,7 +96,7 @@ const _formatAnnotations = (annotations: string[], assemblyId: string) => {
     ['aaRef', 16],
     ['aaAlt', 17],
     ['transcript', 19],
-    ['cdnaPos', 24],
+    ['cdsPos', 26], // actually CDSpos
     ['aaPos', 28],
     ['phred', assemblyId === 'GRCh37' ? 115 : 133],
   ];

diff --git a/server/src/types.ts b/server/src/types.ts
@@ -264,7 +264,7 @@ export interface CaddAnnotation extends VariantCoordinate {
   aaAlt: string;
   aaPos: string;
   aaRef: string;
-  cdnaPos: string;
+  cdsPos: string;
   consequence: string;
   consScore: number;
   phred: number;