+/*
+ * 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
}
else
{
- Cache.log.error("File not found: " + filePath);
+ Console.error("File not found: " + filePath);
}
}
{
final CloseableIterator<VariantContext> it = reader.iterator();
- return new CloseableIterator<>()
+ return new CloseableIterator<VariantContext>()
{
boolean atEnd = false;