Check for null base modification sets when drawing expanded insertion…

…s. See issue #1303
igvteam · Dec 1, 2023 · e92ea91 · e92ea91
1 parent 7bcb418
commit e92ea91
Show file tree

Hide file tree

Showing 2 changed files with 6 additions and 2 deletions.
diff --git a/src/main/java/org/broad/igv/sam/BaseRenderer.java b/src/main/java/org/broad/igv/sam/BaseRenderer.java
@@ -95,7 +95,7 @@ public static void drawExpandedInsertions(InsertionMarker insertionMarker,
 
                     // Compute the start and end of the expanded insertion in pixels
                     int pixelStart = (int) ((insertion.getStart() - origin) / locScale);
-                    int pixelEnd = (int) (pixelStart +  insertion.getLength() / locScale);
+                    int pixelEnd = (int) (pixelStart + insertion.getLength() / locScale);
 
                     // Skip if insertion is out of clipping rectangle -- this probably shouldn't happen
                     if (pixelEnd < rect.x || pixelStart > rect.getMaxX()) {
@@ -150,7 +150,9 @@ public static void drawExpandedInsertions(InsertionMarker insertionMarker,
 
                     if (colorOption.isBaseMod()) {
                         List<BaseModificationSet> baseModificationSets = alignment.getBaseModificationSets();
-                        BaseModificationRenderer.drawBlock(origin, locScale, rect, g, renderOptions, baseModificationSets, insertion);
+                        if (baseModificationSets != null) {
+                            BaseModificationRenderer.drawBlock(origin, locScale, rect, g, renderOptions, baseModificationSets, insertion);
+                        }
                     }
                 }
             }

diff --git a/src/main/java/org/broad/igv/sam/mods/BaseModificationRenderer.java b/src/main/java/org/broad/igv/sam/mods/BaseModificationRenderer.java
@@ -31,6 +31,8 @@ public static void drawModifications(
 
     public static void drawBlock(double bpStart, double locScale, Rectangle rowRect, Graphics g, AlignmentTrack.RenderOptions renderOptions, List<BaseModificationSet> baseModificationSets, AlignmentBlock block) {
 
+        if(baseModificationSets == null) return;
+
         AlignmentTrack.ColorOption colorOption = renderOptions.getColorOption();
         BaseModficationFilter filter = renderOptions.getBasemodFilter();
         float threshold = renderOptions.getBasemodThreshold();