private VCFFileReader reader;
/**
- * Constructor given a raw or compressed VCF file or a (csi or tabix) index file
+ * Constructor given a raw or compressed VCF file or a (csi or tabix) index
+ * file
*
- * 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.
+ * 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
@@ -65,7 +86,7 @@ public class VCFReader implements Closeable, Iterable
}
else
{
- Cache.log.error("File not found: " + filePath);
+ Console.error("File not found: " + filePath);
}
}
@@ -134,8 +155,8 @@ public class VCFReader implements Closeable, Iterable
final String chrom, final int start, final int end)
{
final CloseableIterator it = reader.iterator();
-
- return new CloseableIterator<>()
+
+ return new CloseableIterator()
{
boolean atEnd = false;