add special codec for "bigRmsk" format

Author: jrobinso

src/main/java/org/broad/igv/bbfile/codecs/BBBedCodec.java

@@ -13,18 +13,13 @@
 
 public class BBBedCodec implements BBCodec {
 
-    private final Genome genome;
+
     private final BBUtils.ASTable astable;
 
     int standardFieldCount;
     IGVBEDCodec igvBedCodec;
 
     public BBBedCodec(int standardFieldCount, BBUtils.ASTable autosql) {
-        this(standardFieldCount, autosql, null);
-    }
-
-    public BBBedCodec(int standardFieldCount, BBUtils.ASTable autosql, Genome genome) {
-        this.genome = genome;
         this.astable = autosql;
         this.standardFieldCount = standardFieldCount;
         this.igvBedCodec = new IGVBEDCodec();   // Backing "tribble" codec

src/main/java/org/broad/igv/bbfile/codecs/BBCodecFactory.java

@@ -12,7 +12,12 @@ public static BBCodec getCodec(String autosql, int standardFieldCount) {
         BBUtils.ASTable astable = autosql == null ||
                 autosql.length() == 0 ? null : BBUtils.parseAutosql(autosql);
 
-        return new BBBedCodec(standardFieldCount, astable);
+        switch(astable.name) {
+            case "bigRmskBed":
+                return new BBRmskCodec(standardFieldCount, astable);
+            default:
+                return new BBBedCodec(standardFieldCount, astable);
+        }
 
     }
 }

src/main/java/org/broad/igv/bbfile/codecs/BBRmskCodec.java

@@ -0,0 +1,58 @@
+package org.broad.igv.bbfile.codecs;
+
+import org.broad.igv.bbfile.BBUtils;
+import org.broad.igv.bbfile.BedData;
+import org.broad.igv.feature.BasicFeature;
+
+import java.awt.*;
+import java.util.Map;
+
+public class BBRmskCodec implements BBCodec {
+
+    BBBedCodec bedCodec;
+
+    public BBRmskCodec(int standardFieldCount, BBUtils.ASTable autosql) {
+        bedCodec = new BBBedCodec(standardFieldCount, autosql);
+    }
+
+    @Override
+    public BasicFeature decode(BedData data) {
+        BasicFeature feature = bedCodec.decode(data);
+
+        String name = feature.getName();
+        String repClass = null;
+        String[] parts = name.split("#");
+        if (parts.length > 1) {
+            name = parts[0];
+            repClass = parts[1];
+        }
+
+        feature.setName(name);
+        if (repClass != null) {
+            feature.setAttribute("Repeat Class", repClass);
+            int idx1 = repClass.indexOf("/");
+            String c = idx1 > 0 ? repClass.substring(0, idx1) : repClass;
+            if (c.endsWith("?")) c = c.substring(c.length() - 1);
+            Color color = classColors.containsKey(c) ? classColors.get(c) : defaultColor;
+            feature.setColor(color);
+        }
+
+        return feature;
+    }
+
+
+    static Map<String, Color> classColors = Map.of(
+            "SINE", new Color(31, 119, 180),
+            "LINE", new Color(255, 127, 14),
+            "LTR", new Color(44, 160, 44),
+            "DNA", new Color(214, 39, 40),
+            "Simple", new Color(148, 103, 189),
+            "Low_complexity", new Color(140, 86, 75),
+            "Satellite", new Color(227, 119, 194),
+            "RNA", new Color(127, 127, 127),
+            "Other", new Color(188, 189, 34),
+            "Unknown", new Color(23, 190, 207)
+    );
+
+    static Color defaultColor = new Color(0, 180, 180);
+}

src/test/java/org/broad/igv/bbfile/BBDataSourceTest.java

@@ -115,5 +115,29 @@ public void testBigInteract() throws IOException {
         assertTrue(count > 0);
     }
 
+    // NOTE:  bigInteract is not yet supported in IGV desktop, bigInteract is treated as a plain bed file.
+    @Test
+    public void testBigRmsk() throws IOException {
+
+        String path = "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/bbi/GCA_009914755.4_T2T-CHM13v2.0.t2tRepeatMasker/chm13v2.0_rmsk.bb";
+
+        BBFileReader bbReader = new BBFileReader(path);
+        BBDataSource bbSource = new BBDataSource(bbReader, null);
+
+        String chr = "chr3";
+        int start = 63081504;
+        int end = 64501215;
+
+        Iterator<Feature> iter = bbSource.getFeatures(chr, start, end);
+
+        int count = 0;
+        while (iter.hasNext()) {
+            Feature f = iter.next();
+            assertEquals(chr, f.getChr());
+            assertTrue(f.getStart() <= end && f.getEnd() >= start);
+            count++;
+        }
+        assertTrue(count > 0);
+    }
 
 }