JAL-2738 PoC of Load VCF file on to gene sequence

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

diff --git a/test/jalview/ext/htsjdk/VCFReaderTest.java b/test/jalview/ext/htsjdk/VCFReaderTest.java
index 42c655d..29d752c 100644 (file)
--- a/test/jalview/ext/htsjdk/VCFReaderTest.java
+++ b/test/jalview/ext/htsjdk/VCFReaderTest.java
@@ -26,6 +26,8 @@ public class VCFReaderTest
   // 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 to exercise some basic functionality of the htsjdk VCF reader
    * 
@@ -105,8 +107,6 @@ public class VCFReaderTest
     pw.close();
     return f;
   }
-
-  // "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
@@ -131,15 +131,29 @@ public class VCFReaderTest
     CloseableIterator<VariantContext> features = reader.query("17",
             43128978 + 9724, 43128978 + 9734); // first 11 CDS positions
 
-    assertEquals(features.next().getStart(), 43138702);
-    assertEquals(features.next().getStart(), 43138704);
-    assertEquals(features.next().getStart(), 43138707);
-    assertEquals(features.next().getStart(), 43138708);
-    assertEquals(features.next().getStart(), 43138710);
-    assertEquals(features.next().getStart(), 43138711);
+    assertEquals(printNext(features), 43138702);
+    assertEquals(printNext(features), 43138704);
+    assertEquals(printNext(features), 43138707);
+    assertEquals(printNext(features), 43138708);
+    assertEquals(printNext(features), 43138710);
+    assertEquals(printNext(features), 43138711);
     assertFalse(features.hasNext());
 
     features.close();
     reader.close();
   }
+
+  /**
+   * Prints the toString value of the next variant, and returns its start
+   * location
+   * 
+   * @param features
+   * @return
+   */
+  protected int printNext(CloseableIterator<VariantContext> features)
+  {
+    VariantContext next = features.next();
+    System.out.println(next.toString());
+    return next.getStart();
+  }
 }