Enable linked read preferences, previously these were no-ops (#1645)

igvteam · Jan 25, 2025 · a37cff6 · a37cff6
1 parent 6429dac
commit a37cff6
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Showing 6 changed files with 19 additions and 17 deletions.
diff --git a/src/main/java/org/broad/igv/prefs/Constants.java b/src/main/java/org/broad/igv/prefs/Constants.java
@@ -154,6 +154,8 @@ private Constants() {
     public static final String SAM_COLOR_BY_TAG = "SAM.COLOR_BY_TAG";
     public static final String SAM_SORT_BY_TAG = "SAM.SORT_BY_TAG";
     public static final String SAM_GROUP_BY_TAG = "SAM.GROUP_BY_TAG";
+    public static final String SAM_LINKED_READS = "SAM.LINK_READS";
+    public static final String SAM_LINK_TAG = "SAM.LINK_TAG";
     public static final String SAM_LINK_BY_TAGS = "SAM.LINK_BY_TAGS";
     public static final String SAM_GROUP_BY_POS = "SAM.GROUP_BY_POS";
     public static final String SAM_BISULFITE_CONTEXT = "SAM.BISULFITE_CONTEXT";

diff --git a/src/main/java/org/broad/igv/sam/AlignmentTrack.java b/src/main/java/org/broad/igv/sam/AlignmentTrack.java
@@ -1061,7 +1061,7 @@ void setLinkedReadView(boolean linkedReads, String tag) {
     }
 
     /**
-     * Detect if we are in linked-read view
+     * Detect if we are in linked-read view (10X Loupe style view)
      */
     boolean isLinkedReadView() {
         return renderOptions != null &&
@@ -1548,7 +1548,7 @@ public boolean isInvertGroupSorting() {
         }
 
         public String getLinkByTag() {
-            return linkByTag;
+            return linkByTag == null ? getPreferences().get(SAM_LINK_TAG) : linkByTag;
         }
 
         public GroupOption getGroupByOption() {
@@ -1564,7 +1564,7 @@ public GroupOption getGroupByOption() {
         }
 
         public boolean isLinkedReads() {
-            return linkedReads != null && linkedReads;
+            return linkedReads == null ? getPreferences().getAsBoolean(SAM_LINKED_READS) : linkedReads;
         }
 
         public boolean isQuickConsensusMode() {

diff --git a/src/main/java/org/broad/igv/sam/AlignmentTrackMenu.java b/src/main/java/org/broad/igv/sam/AlignmentTrackMenu.java
@@ -1162,16 +1162,6 @@ void addLinkedReadItems() {
         add(linkByTagItem);
     }
 
-    private JCheckBoxMenuItem linkedReadViewItem(String tag) {
-        final JCheckBoxMenuItem item = new JCheckBoxMenuItem("Linked read view (" + tag + ")");
-        item.setSelected(alignmentTrack.isLinkedReadView() && tag != null && tag.equals(renderOptions.getLinkByTag()));
-        item.addActionListener(aEvt -> {
-            boolean linkedReads = item.isSelected();
-            alignmentTrack.setLinkedReadView(linkedReads, tag);
-        });
-        return item;
-    }
-
     private JCheckBoxMenuItem linkedReadItem(String tag) {
         final JCheckBoxMenuItem item = new JCheckBoxMenuItem("Link by " + tag);
         item.setSelected(!alignmentTrack.isLinkedReadView() && alignmentTrack.isLinkedReads() && tag.equals(renderOptions.getLinkByTag()));

diff --git a/src/main/java/org/broad/igv/sam/LinkedAlignment.java b/src/main/java/org/broad/igv/sam/LinkedAlignment.java
@@ -1,5 +1,7 @@
 package org.broad.igv.sam;
 
+import htsjdk.samtools.SAMRecord;
+import htsjdk.samtools.SAMTag;
 import org.broad.igv.Globals;
 import org.broad.igv.feature.Strand;
 import org.broad.igv.track.WindowFunction;
@@ -299,7 +301,7 @@ public boolean isPrimary() {
 
     @Override
     public boolean isSupplementary() {
-        return false;
+        return true;
     }
 
     @Override

diff --git a/src/main/java/org/broad/igv/sam/SAMAlignment.java b/src/main/java/org/broad/igv/sam/SAMAlignment.java
@@ -56,8 +56,6 @@
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import static org.broad.igv.prefs.Constants.SAM_HIDE_SMALL_INDEL;
-
 /**
  * @author jrobinso
  */
@@ -225,6 +223,12 @@ public Object getAttribute(String key) {
         }
     }
 
+    public List<SAMRecord.SAMTagAndValue> getAttributes() {
+        return record.getAttributes();
+    }
+
+
+
     private Object getAttribute(SAMTag key) {
         return key == null ? null : record.getAttribute(key);
     }

diff --git a/src/main/resources/org/broad/igv/prefs/preferences.tab b/src/main/resources/org/broad/igv/prefs/preferences.tab
@@ -107,9 +107,13 @@ SAM.ALLELE_USE_QUALITY	Quality weight allele fraction	boolean	TRUE
 
 SAM.COLOR_BY	Color alignments by	select NONE|READ_STRAND|FIRST_OF_PAIR_STRAND|PAIR_ORIENTATION|UNEXPECTED_PAIR|INSERT_SIZE|BASE_MODIFICATION|BASE_MODIFICATION_2COLOR|SAMPLE|READ_GROUP|LIBRARY|MOVIE|ZMW|BISULFITE|NOMESEQ|TAG|MAPPED_SIZE|LINK_STRAND|YC_TAG|READ_ORDER	UNEXPECTED_PAIR
 SAM.COLOR_BY_TAG	Color by TAG	string
+---
 SAM.GROUP_OPTION	Group alignments by	select NONE|STRAND|SAMPLE|READ_GROUP|LIBRARY|FIRST_OF_PAIR_STRAND|TAG|PAIR_ORIENTATION|MATE_CHROMOSOME|SV_ALIGNMENT|SUPPLEMENTARY|BASE_AT_POS|MOVIE|ZMW|HAPLOTYPE|READ_ORDER|LINKED|PHASE|MAPPING_QUALITY|DUPLICATE
 SAM.GROUP_BY_TAG	Group by TAG	string
-SAM.GROUP_ALL	Syncrohize alignment track grouping	boolean	FALSE
+SAM.GROUP_ALL	Syncronize grouping across all alignment tracks	boolean	FALSE
+---
+SAM.LINK_READS	Link alignments by tag	boolean	FALSE
+SAM.LINK_TAG	Linking tag	string	READNAME
 
 SAM.QUALITY_THRESHOLD	Mapping quality threshold	int	0	Hide alignments with MQ lower than this value
 SAM.ALIGNMENT_SCORE_THRESHOLD	Alignment score threshold (AS tag)	int	0