JAL-1793 wrapper for plain or indexed VCF + simple tests

[jalview.git] / test / jalview / ext / htsjdk / TabixFeatureReaderTest.java

diff --git a/test/jalview/ext/htsjdk/TabixFeatureReaderTest.java b/test/jalview/ext/htsjdk/TabixFeatureReaderTest.java
deleted file mode 100644 (file)
index 48a932e..0000000
--- a/test/jalview/ext/htsjdk/TabixFeatureReaderTest.java
+++ /dev/null
@@ -1,51 +0,0 @@
-package jalview.ext.htsjdk;
-
-import htsjdk.tribble.CloseableTribbleIterator;
-import htsjdk.tribble.TabixFeatureReader;
-import htsjdk.variant.variantcontext.VariantContext;
-import htsjdk.variant.vcf.VCFCodec;
-
-import java.io.IOException;
-
-import org.testng.annotations.Test;
-
-public class TabixFeatureReaderTest
-{
-  // gnomAD exome variant dataset
-  private static final String VCF_PATH = "/Volumes/gjb/smacgowan/NOBACK/resources/gnomad/gnomad.exomes.r2.0.1.sites.vcf.gz";
-
-  // "https://storage.cloud.google.com/gnomad-public/release/2.0.1/vcf/exomes/gnomad.exomes.r2.0.1.sites.vcf.gz";
-
-  /**
-   * A 'test' that demonstrates querying an indexed VCF file for features in a
-   * specified interval
-   * 
-   * @throws IOException
-   */
-  @Test
-  public void testQuery() throws IOException
-  {
-    /*
-     * if not specified, assumes index file is filename.tbi
-     */
-    TabixFeatureReader<VariantContext, VCFCodec> reader = new TabixFeatureReader<>(
-            VCF_PATH, VCF_PATH, new VCFCodec());
-
-    /*
-     * gene NMT1 (human) is on chromosome 17
-     * GCHR38 (Ensembl): 45051610-45109016
-     * GCHR37 (gnoMAD): 43128978-43186384
-     * CDS begins at offset 9720, first CDS variant at offset 9724
-     */
-    CloseableTribbleIterator<VariantContext> features = reader.query("17",
-            43128978 + 9724, 43128978 + 9734); // first 11 CDS positions
-    while (features.hasNext())
-    {
-      System.out.println(features.next().toString());
-    }
-
-    features.close();
-    reader.close();
-  }
-
-}