From 4059e928442daa03c90161737e40f488d8da6bbf Mon Sep 17 00:00:00 2001
From: Colin <colin.diesh@gmail.com>
Date: Thu, 14 Nov 2024 13:12:45 -0500
Subject: [PATCH] Revert no_ref support temporarily, might need to get a better
 understanding of MD tag usage
 https://github.com/galaxyproject/tools-iuc/issues/6523

---
 .../CramAdapter/CramSlightlyLazyFeature.ts    | 25 ++++++++++---------
 1 file changed, 13 insertions(+), 12 deletions(-)

diff --git a/plugins/alignments/src/CramAdapter/CramSlightlyLazyFeature.ts b/plugins/alignments/src/CramAdapter/CramSlightlyLazyFeature.ts
index 354ff92b3f..ac6c2b9798 100644
--- 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 {