X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fhtsjdk%2FVCFReader.java;h=2859e0f7ae297bfb6649393ace4c73769c7879bd;hb=3637bb169b4516a56818137e40cc6eff6cd4b969;hp=c5e09e041376e13ed1691bfe727b963f2b5c3d6b;hpb=9317cd655af4803461acc71581ecbdc0a6677069;p=jalview.git

diff --git a/src/jalview/ext/htsjdk/VCFReader.java b/src/jalview/ext/htsjdk/VCFReader.java
index c5e09e0..2859e0f 100644
--- a/src/jalview/ext/htsjdk/VCFReader.java
+++ b/src/jalview/ext/htsjdk/VCFReader.java
@@ -1,14 +1,16 @@
 package jalview.ext.htsjdk;
 
-import htsjdk.samtools.util.CloseableIterator;
-import htsjdk.variant.variantcontext.VariantContext;
-import htsjdk.variant.vcf.VCFFileReader;
-import htsjdk.variant.vcf.VCFHeader;
+import jalview.bin.Cache;
 
 import java.io.Closeable;
 import java.io.File;
 import java.io.IOException;
 
+import htsjdk.samtools.util.CloseableIterator;
+import htsjdk.variant.variantcontext.VariantContext;
+import htsjdk.variant.vcf.VCFFileReader;
+import htsjdk.variant.vcf.VCFHeader;
+
 /**
  * A thin wrapper for htsjdk classes to read either plain, or compressed, or
  * compressed and indexed VCF files
@@ -19,36 +21,52 @@ public class VCFReader implements Closeable, Iterable<VariantContext>
 
   private static final String TBI_EXTENSION = ".tbi";
 
+  private static final String CSI_EXTENSION = ".csi";
+
   private boolean indexed;
 
   private VCFFileReader reader;
 
   /**
-   * Constructor given a raw or compressed VCF file or a (tabix) index file
+   * Constructor given a raw or compressed VCF file or a (csi or tabix) index file
    * <p>
-   * For now, file type is inferred from its suffix: .gz or .bgz for compressed
-   * data, .tbi for an index file, anything else is assumed to be plain text
-   * VCF.
+   * If the file path ends in ".tbi" or ".csi", <em>or</em> appending one of these
+   * extensions gives a valid file path, open as indexed, else as unindexed.
    * 
    * @param f
    * @throws IOException
    */
   public VCFReader(String filePath) throws IOException
   {
-    if (filePath.endsWith(GZ))
+    indexed = false;
+    if (filePath.endsWith(TBI_EXTENSION)
+            || filePath.endsWith(CSI_EXTENSION))
     {
-      if (new File(filePath + TBI_EXTENSION).exists())
-      {
-        indexed = true;
-      }
+      indexed = true;
+      filePath = filePath.substring(0, filePath.length() - 4);
     }
-    else if (filePath.endsWith(TBI_EXTENSION))
+    else if (new File(filePath + TBI_EXTENSION).exists())
+    {
+      indexed = true;
+    }
+    else if (new File(filePath + CSI_EXTENSION).exists())
     {
       indexed = true;
-      filePath = filePath.substring(0, filePath.length() - 4);
     }
 
-    reader = new VCFFileReader(new File(filePath), indexed);
+    /*
+     * we pass the name of the unindexed file to htsjdk,
+     * with a flag to assert whether it is indexed
+     */
+    File file = new File(filePath);
+    if (file.exists())
+    {
+      reader = new VCFFileReader(file, indexed);
+    }
+    else
+    {
+      Cache.log.error("File not found: " + filePath);
+    }
   }
 
   @Override
@@ -72,9 +90,10 @@ public class VCFReader implements Closeable, Iterable<VariantContext>
 
   /**
    * Queries for records overlapping the region specified. Note that this method
-   * requires a VCF file with an associated index. If no index exists a
-   * TribbleException will be thrown. Client code should call close() on the
-   * iterator when finished with it.
+   * is performant if the VCF file is indexed, and may be very slow if it is
+   * not.
+   * <p>
+   * Client code should call close() on the iterator when finished with it.
    * 
    * @param chrom
    *          the chromosome to query
@@ -87,7 +106,108 @@ public class VCFReader implements Closeable, Iterable<VariantContext>
   public CloseableIterator<VariantContext> query(final String chrom,
           final int start, final int end)
   {
-    return reader == null ? null : reader.query(chrom, start, end);
+    if (reader == null)
+    {
+      return null;
+    }
+    if (indexed)
+    {
+      return reader.query(chrom, start, end);
+    }
+    else
+    {
+      return queryUnindexed(chrom, start, end);
+    }
+  }
+
+  /**
+   * Returns an iterator over variant records read from a flat file which
+   * overlap the specified chromosomal positions. Call close() on the iterator
+   * when finished with it!
+   * 
+   * @param chrom
+   * @param start
+   * @param end
+   * @return
+   */
+  protected CloseableIterator<VariantContext> queryUnindexed(
+          final String chrom, final int start, final int end)
+  {
+    final CloseableIterator<VariantContext> it = reader.iterator();
+    
+    return new CloseableIterator<VariantContext>()
+    {
+      boolean atEnd = false;
+
+      // prime look-ahead buffer with next matching record
+      private VariantContext next = findNext();
+
+      private VariantContext findNext()
+      {
+        if (atEnd)
+        {
+          return null;
+        }
+        VariantContext variant = null;
+        while (it.hasNext())
+        {
+          variant = it.next();
+          int vstart = variant.getStart();
+
+          if (vstart > end)
+          {
+            atEnd = true;
+            close();
+            return null;
+          }
+
+          int vend = variant.getEnd();
+          // todo what is the undeprecated way to get
+          // the chromosome for the variant?
+          if (chrom.equals(variant.getContig()) && (vstart <= end)
+                  && (vend >= start))
+          {
+            return variant;
+          }
+        }
+        return null;
+      }
+
+      @Override
+      public boolean hasNext()
+      {
+        boolean hasNext = !atEnd && (next != null);
+        if (!hasNext)
+        {
+          close();
+        }
+        return hasNext;
+      }
+
+      @Override
+      public VariantContext next()
+      {
+        /*
+         * return the next match, and then re-prime
+         * it with the following one (if any)
+         */
+        VariantContext temp = next;
+        next = findNext();
+        return temp;
+      }
+
+      @Override
+      public void remove()
+      {
+        // not implemented
+      }
+
+      @Override
+      public void close()
+      {
+        it.close();
+      }
+    };
   }
 
   /**
@@ -99,4 +219,15 @@ public class VCFReader implements Closeable, Iterable<VariantContext>
   {
     return reader == null ? null : reader.getFileHeader();
   }
+
+  /**
+   * Answers true if we are processing a tab-indexed VCF file, false if it is a
+   * plain text (uncompressed) file.
+   * 
+   * @return
+   */
+  public boolean isIndex()
+  {
+    return indexed;
+  }
 }