Revert no_ref support temporarily, might need to get a better

understanding of MD tag usage galaxyproject/tools-iuc#6523
GMOD · Nov 14, 2024 · 4059e92 · 4059e92
1 parent b131722
commit 4059e92
Showing 1 changed file with 13 additions and 12 deletions.
diff --git a/plugins/alignments/src/CramAdapter/CramSlightlyLazyFeature.ts b/plugins/alignments/src/CramAdapter/CramSlightlyLazyFeature.ts
@@ -124,22 +124,23 @@ export default class CramSlightlyLazyFeature implements Feature {
   }
 
   get mismatches() {
-    const mismatches = readFeaturesToMismatches(
+    return readFeaturesToMismatches(
       this.record.readFeatures,
       this.start,
       this.qualRaw,
     )
-    return this.tags.MD && this.seq
-      ? mismatches.concat(
-          mdToMismatches(
-            this.tags.MD,
-            parseCigar(this.CIGAR),
-            mismatches,
-            this.seq,
-            this.qualRaw,
-          ),
-        )
-      : mismatches
+    // this commented code can try to resolve MD tags, xref https://github.com/galaxyproject/tools-iuc/issues/6523#issuecomment-2462927211 but put on hold
+    // return this.tags.MD && this.seq
+    //   ? mismatches.concat(
+    //       mdToMismatches(
+    //         this.tags.MD,
+    //         parseCigar(this.CIGAR),
+    //         mismatches,
+    //         this.seq,
+    //         this.qualRaw,
+    //       ),
+    //     )
+    //   : mismatches
   }
 
   get fields(): SimpleFeatureSerialized {