Implement reader for UCSC ".2bit" sequence format

igvteam · Oct 2, 2023 · dcee1f1 · dcee1f1
1 parent e76048d
commit dcee1f1
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Showing 30 changed files with 438 additions and 63,605 deletions.
diff --git a/src/main/java/org/broad/igv/feature/genome/ColorSpaceSequence.java b/src/main/java/org/broad/igv/feature/genome/ColorSpaceSequence.java
@@ -51,7 +51,7 @@ public ColorSpaceSequence(Sequence sequence) {
     public byte[] getSequence(String chr, int start, int end) {
         // We need to know the base just to the left of the start
         int csStart = (start == 0 ? 0 : start - 1);
-        byte[] baseSequence = sequence.getSequence(chr, csStart, end, true);
+        byte[] baseSequence = sequence.getSequence(chr, csStart, end);
         if (baseSequence == null || baseSequence.length == 0) {
             return baseSequence;
         }

diff --git a/src/main/java/org/broad/igv/feature/genome/Genome.java b/src/main/java/org/broad/igv/feature/genome/Genome.java
@@ -455,15 +455,7 @@ public byte[] getSequence(String chr, int start, int end, boolean useCache) {
         if (end <= start) {
             return null;
         }
-        return sequence.getSequence(chr, start, end, useCache);
-    }
-
-    public boolean sequenceIsRemote() {
-        return sequence.isRemote();
-    }
-
-    public boolean sequenceIsFasta() {
-        return sequence.isFasta();
+        return sequence.getSequence(chr, start, end);
     }
 
     public String getDisplayName() {
@@ -633,11 +625,6 @@ private static synchronized String getSpeciesForID(String id) {
         ucsdIDMap.put("b37", "hg19");
     }
 
-
-    public boolean sequenceIsLoaded(ReferenceFrame frame) {
-        return sequence.isLoaded(frame);
-    }
-
     public void setAnnotationResources(List<ResourceLocator> annotationResources) {
         this.annotationResources = annotationResources;
     }

diff --git a/src/main/java/org/broad/igv/feature/genome/IGVSequence.java b/src/main/java/org/broad/igv/feature/genome/IGVSequence.java
diff --git a/src/main/java/org/broad/igv/feature/genome/InMemorySequence.java b/src/main/java/org/broad/igv/feature/genome/InMemorySequence.java
@@ -46,7 +46,7 @@ public InMemorySequence(String chr, byte[] seq) {
         sequenceMap.put(chr, seq);
     }
 
-    public byte[] getSequence(String chr, int qstart, int qend, boolean useCache) {
+    public byte[] getSequence(String chr, int qstart, int qend) {
         byte[] allBytes = sequenceMap.get(chr);
         if (allBytes == null) {
             return null;
@@ -86,8 +86,4 @@ public int getChromosomeLength(String chrname) {
         return bytes == null ? 0 : bytes.length;
     }
 
-    @Override
-    public boolean isRemote() {
-        return false;
-    }
 }
diff --git a/src/main/java/org/broad/igv/feature/genome/Sequence.java b/src/main/java/org/broad/igv/feature/genome/Sequence.java
@@ -37,19 +37,12 @@
  */
 public interface Sequence {
 
-    byte[] getSequence(String chr, int start, int end, boolean useCache);
+    byte[] getSequence(String chr, int start, int end);
 
     byte getBase(String chr, int position);
 
     List<String> getChromosomeNames();
 
     int getChromosomeLength(String chrname);
 
-    default boolean isLoaded(ReferenceFrame frame) {
-        return false;
-    }
-
-    boolean isRemote();
-
-    default boolean isFasta() {return false;}
 }
diff --git a/src/main/java/org/broad/igv/feature/genome/SequenceWrapper.java b/src/main/java/org/broad/igv/feature/genome/SequenceWrapper.java
@@ -87,43 +87,17 @@ public int getChromosomeLength(String chrname) {
         return sequence.getChromosomeLength(chrname);
     }
 
-    @Override
-    public boolean isLoaded(ReferenceFrame frame) {
-        if (!cacheSequences) return false;
-
-        int startTile = (int) frame.getOrigin() / tileSize;
-        int endTile = (int) frame.getEnd() / tileSize;
-        String chr = frame.getChrName();
-        for (int i = startTile; i <= endTile; i++) {
-            String key = getKey(chr, i);
-            if (!sequenceCache.containsKey(key)) return false;
-
-        }
-        return true;
-    }
-
-    @Override
-    public boolean isRemote() {
-        return sequence.isRemote();
-    }
-
-    @Override
-    public boolean isFasta() {
-        return sequence.isFasta();
-    }
-
     /**
      * Return the reference dna sequence for the exact interval specified.
      *
      * @param chr
      * @param start
      * @param end
-     * @param useCache
      * @return
      */
-    public byte[] getSequence(String chr, int start, int end, boolean useCache) {
+    public byte[] getSequence(String chr, int start, int end) {
 
-        if (cacheSequences && useCache) {
+        if (cacheSequences) {
             byte[] seqbytes = new byte[end - start];
 
             int startTile = start / tileSize;
@@ -170,7 +144,7 @@ public byte[] getSequence(String chr, int start, int end, boolean useCache) {
 
             return seqbytes;
         } else {
-            return sequence.getSequence(chr, start, end, useCache);
+            return sequence.getSequence(chr, start, end);
         }
     }
 
@@ -187,7 +161,7 @@ private SequenceTile getSequenceTile(String chr, int tileNo) {
                 return null;
             }
 
-            byte[] seq = sequence.getSequence(chr, start, end, true);
+            byte[] seq = sequence.getSequence(chr, start, end);
             tile = new SequenceTile(start, seq);
             sequenceCache.put(key, tile);
         }
@@ -235,7 +209,7 @@ private SequenceTile[] getSequenceTiles(String chr, int startTile, int endTile)
     private void loadTiles(String chr, int startTile, SequenceTile[] tiles, TileRange toLoad) {
         int start = toLoad.startTile * tileSize;
         int end = (toLoad.endTile + 1) * tileSize;
-        byte[] seq = sequence.getSequence(chr, start, end, true);
+        byte[] seq = sequence.getSequence(chr, start, end);
 
         if(seq == null) {
             log.warn("Null sequence for " + chr + ":" + start + "-" + end);