X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fhtsjdk%2FVCFReaderTest.java;fp=test%2Fjalview%2Fext%2Fhtsjdk%2FVCFReaderTest.java;h=e3bef41bd6745903f8aa252b78612576cc3e3852;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=bf617aec97ba4293decec6a3bab85cd05d2b3d99;hpb=e7338a61f3ce96dadf44ac80b2b32cc5ba4b94c8;p=jalview.git

diff --git a/test/jalview/ext/htsjdk/VCFReaderTest.java b/test/jalview/ext/htsjdk/VCFReaderTest.java
index bf617ae..e3bef41 100644
--- a/test/jalview/ext/htsjdk/VCFReaderTest.java
+++ b/test/jalview/ext/htsjdk/VCFReaderTest.java
@@ -16,8 +16,7 @@ import org.testng.annotations.Test;
 
 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
@@ -102,13 +101,14 @@ public class VCFReaderTest
     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
@@ -122,7 +122,7 @@ public class VCFReaderTest
      * 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
@@ -159,7 +159,7 @@ public class VCFReaderTest
   }
 
   // "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
    * 
@@ -175,7 +175,7 @@ public class VCFReaderTest
      * query for overlap of 5-8 - should find variant at 7
      */
     CloseableIterator<VariantContext> variants = reader.query("20", 5, 8);
-  
+
     /*
      * INDEL G/GA variant
      */