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igvteam · Aug 15, 2024 · bdeaf1c · bdeaf1c
1 parent 9a43070
commit bdeaf1c
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Showing 3 changed files with 7 additions and 9 deletions.
diff --git a/src/main/java/org/broad/igv/sam/AlignmentRenderer.java b/src/main/java/org/broad/igv/sam/AlignmentRenderer.java
@@ -758,7 +758,7 @@ private void drawAlignment(
                     else if (block.getCigarOperator() == 'X') g = context.getGraphics2D("MISMATCH");
                 }
 
-                if(renderOptions.getDuplicatesOption() == AlignmentTrack.DuplicatesOption.TEXTURED && alignment.isDuplicate()) {
+                if(renderOptions.getDuplicatesOption() == AlignmentTrack.DuplicatesOption.TEXTURE && alignment.isDuplicate()) {
                     final Graphics2D tg = (Graphics2D) g.create();
 
                     final TexturePaint tp = getDuplicateTexture(tg.getColor());

diff --git a/src/main/java/org/broad/igv/sam/AlignmentTileLoader.java b/src/main/java/org/broad/igv/sam/AlignmentTileLoader.java
@@ -26,7 +26,6 @@
 package org.broad.igv.sam;
 
 import htsjdk.samtools.SAMFileHeader;
-import htsjdk.samtools.SAMTag;
 import htsjdk.samtools.util.CloseableIterator;
 import org.broad.igv.event.IGVEvent;
 import org.broad.igv.logging.*;
@@ -43,7 +42,6 @@
 import org.broad.igv.util.ObjectCache;
 import org.broad.igv.util.RuntimeUtils;
 
-import javax.swing.*;
 import java.io.IOException;
 import java.lang.ref.WeakReference;
 import java.text.DecimalFormat;
@@ -135,7 +133,7 @@ AlignmentTile loadTile(String chr,
         boolean filterSupplementaryAlignments = prefMgr.getAsBoolean(SAM_FILTER_SUPPLEMENTARY_ALIGNMENTS);
         ReadGroupFilter filter = ReadGroupFilter.getFilter();
         boolean filterDuplicates = renderOptions != null
-                ? renderOptions.getDuplicatesOption() == AlignmentTrack.DuplicatesOption.FILTERED
+                ? renderOptions.getDuplicatesOption() == AlignmentTrack.DuplicatesOption.FILTER
                 : prefMgr.getAsBoolean(SAM_FILTER_DUPLICATES);
 
         int qualityThreshold = prefMgr.getAsInt(SAM_QUALITY_THRESHOLD);

diff --git a/src/main/java/org/broad/igv/sam/AlignmentTrack.java b/src/main/java/org/broad/igv/sam/AlignmentTrack.java
@@ -136,9 +136,9 @@ public boolean isSMRTKinetics() {
     }
 
     public enum DuplicatesOption {
-        FILTERED("filtered", true),
-        VISIBLE("visible", false),
-        TEXTURED("textured", false);
+        FILTER("filter duplicates", true),
+        SHOW("show duplicates", false),
+        TEXTURE("texture duplicates", false);
 
         public final String label;
         public final boolean filtered;
@@ -1493,8 +1493,8 @@ public DuplicatesOption getDuplicatesOption() {
                 return duplicatesOption;
             } else {
                 duplicatesOption = prefs.getAsBoolean(SAM_FILTER_DUPLICATES)
-                        ? DuplicatesOption.FILTERED
-                        : DuplicatesOption.VISIBLE;
+                        ? DuplicatesOption.FILTER
+                        : DuplicatesOption.SHOW;
             }
             return duplicatesOption;
         }