Look for "TS" attribute to determine transcript strand. See #1558

igvteam · Sep 4, 2024 · 15d7569 · 15d7569
1 parent 7aca9ea
commit 15d7569
Showing 1 changed file with 5 additions and 1 deletion.
diff --git a/src/main/java/org/broad/igv/sam/SpliceJunctionHelper.java b/src/main/java/org/broad/igv/sam/SpliceJunctionHelper.java
@@ -110,7 +110,11 @@ public void addAlignment(Alignment alignment) {
 
         // Determine strand.  First check for explicit attribute.
         boolean isNegativeStrand;
-        Object strandAttr = alignment.getAttribute("XS");
+        Object strandAttr = alignment.getAttribute("TS");
+        if(strandAttr == null) {
+            strandAttr = alignment.getAttribute("XS");   // Older convention
+        }
+
         if (strandAttr != null) {
             isNegativeStrand = strandAttr.toString().charAt(0) == '-';
         } else {