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
*
- * 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", or 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
+ {
+ Console.error("File not found: " + filePath);
+ }
}
@Override
@@ -72,9 +109,10 @@ public class VCFReader implements Closeable, Iterable
/**
* 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.
+ *
+ * Client code should call close() on the iterator when finished with it.
*
* @param chrom
* the chromosome to query
@@ -87,7 +125,108 @@ public class VCFReader implements Closeable, Iterable
public CloseableIterator 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 queryUnindexed(
+ final String chrom, final int start, final int end)
+ {
+ final CloseableIterator it = reader.iterator();
+
+ return new CloseableIterator()
+ {
+ 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 +238,15 @@ public class VCFReader implements Closeable, Iterable
{
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;
+ }
}