+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ext.htsjdk;
-import jalview.bin.Cache;
-
import java.io.Closeable;
import java.io.File;
import java.io.IOException;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.vcf.VCFFileReader;
import htsjdk.variant.vcf.VCFHeader;
+import jalview.bin.Console;
/**
* A thin wrapper for htsjdk classes to read either plain, or compressed, or
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
* <p>
- * 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.
+ * 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
}
else
{
- Cache.log.error("File not found: " + filePath);
+ Console.error("File not found: " + filePath);
}
}
final String chrom, final int start, final int end)
{
final CloseableIterator<VariantContext> it = reader.iterator();
-
+
return new CloseableIterator<VariantContext>()
{
boolean atEnd = false;