+/*
+ * 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 static org.testng.Assert.assertEquals;
public class VCFReaderTest
{
- private static final String[] VCF = new String[] {
- "##fileformat=VCFv4.2",
+ private static final String[] VCF = new String[] { "##fileformat=VCFv4.2",
"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO",
"20\t3\t.\tC\tG\t.\tPASS\tDP=100", // SNP C/G
"20\t7\t.\tG\tGA\t.\tPASS\tDP=100", // insertion G/GA
File f = File.createTempFile("Test", "vcf");
f.deleteOnExit();
PrintWriter pw = new PrintWriter(f);
- for (String vcfLine : VCF) {
+ for (String vcfLine : VCF)
+ {
pw.println(vcfLine);
}
pw.close();
return f;
}
-
+
/**
* A 'test' that demonstrates querying an indexed VCF file for features in a
* specified interval
* if not specified, assumes index file is filename.tbi
*/
VCFReader reader = new VCFReader(VCF_PATH);
-
+
/*
* gene NMT1 (human) is on chromosome 17
* GCHR38 (Ensembl): 45051610-45109016
}
// "https://storage.cloud.google.com/gnomad-public/release/2.0.1/vcf/exomes/gnomad.exomes.r2.0.1.sites.vcf.gz";
-
+
/**
* Test the query method that wraps a non-indexed VCF file
*
* query for overlap of 5-8 - should find variant at 7
*/
CloseableIterator<VariantContext> variants = reader.query("20", 5, 8);
-
+
/*
* INDEL G/GA variant
*/