Add sort alignments by readname. Fixes #419

igvteam · Mar 20, 2020 · 0e6a0e3 · ollenordesjo · Mar 16, 2021 · 0e6a0e3
1 parent f95cb2c
commit 0e6a0e3
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Showing 5 changed files with 8 additions and 2 deletions.
diff --git a/src/main/java/org/broad/igv/batch/CommandExecutor.java b/src/main/java/org/broad/igv/batch/CommandExecutor.java
@@ -921,6 +921,8 @@ private static AlignmentTrack.SortOption getAlignmentSortOption(String str) {
             return AlignmentTrack.SortOption.MATE_CHR;
         } else if (str.equalsIgnoreCase("readOrder")) {
             return AlignmentTrack.SortOption.READ_ORDER;
+        } else if (str.equalsIgnoreCase("readname")) {
+            return AlignmentTrack.SortOption.READ_NAME;
         } else {
             try {
                 return AlignmentTrack.SortOption.valueOf(str.toUpperCase());

diff --git a/src/main/java/org/broad/igv/sam/AlignmentTrack.java b/src/main/java/org/broad/igv/sam/AlignmentTrack.java
@@ -96,7 +96,7 @@ enum ColorOption {
 
     public enum SortOption {
         START, STRAND, NUCLEOTIDE, QUALITY, SAMPLE, READ_GROUP, INSERT_SIZE, FIRST_OF_PAIR_STRAND, MATE_CHR, TAG,
-        SUPPLEMENTARY, NONE, HAPLOTYPE, READ_ORDER
+        SUPPLEMENTARY, NONE, HAPLOTYPE, READ_ORDER, READ_NAME
     }
 
     public enum GroupOption {
@@ -1633,6 +1633,7 @@ void addSortMenuItem() {
             mappings.put("sample", SortOption.SAMPLE);
             mappings.put("read group", SortOption.READ_GROUP);
             mappings.put("read order", SortOption.READ_ORDER);
+            mappings.put("read name", SortOption.READ_NAME);
 
             if (dataManager.isPairedEnd()) {
                 mappings.put("insert size", SortOption.INSERT_SIZE);

diff --git a/src/main/java/org/broad/igv/sam/Row.java b/src/main/java/org/broad/igv/sam/Row.java
@@ -97,7 +97,6 @@ public double calculateScore(AlignmentTrack.SortOption option, double center, Al
                     else {
                         score = 0;
                     }
-
                     return score;
                 case NUCLEOTIDE:
                     byte base = centerAlignment.getBase(adjustedCenter);
@@ -172,6 +171,10 @@ public double calculateScore(AlignmentTrack.SortOption option, double center, Al
                     //String hapname = centerAlignment.getHaplotypeName();
                     //return hapname == null ? 0 : hapname.hashCode();
                     return centerAlignment.getHapDistance();
+                case READ_NAME:
+                    String readName = centerAlignment.getReadName();
+                    score = readName == null ? 0 : readName.hashCode();
+                    return score;
                 default:
                     return Integer.MAX_VALUE;
 

diff --git a/sv.png b/sv.png
diff --git a/test.png b/test.png