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=befdab1399520e88c745399c9146e6ff341cf4ed;hb=9c98d4bd666346f6ad3892c5394b7da3be82d93e;hp=bf617aec97ba4293decec6a3bab85cd05d2b3d99;hpb=c7b2143c9cf7c5e05ad63251f7d3910751b16d20;p=jalview.git

diff --git a/test/jalview/ext/htsjdk/VCFReaderTest.java b/test/jalview/ext/htsjdk/VCFReaderTest.java
index bf617ae..befdab1 100644
--- a/test/jalview/ext/htsjdk/VCFReaderTest.java
+++ b/test/jalview/ext/htsjdk/VCFReaderTest.java
@@ -1,3 +1,23 @@
+/*
+ * 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;
@@ -16,8 +36,7 @@ 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 +121,14 @@ 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 +142,7 @@ 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 +179,7 @@ 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 +195,7 @@ 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
      */