JAL-1793 spike branch updated to latest

[jalview.git] / test / jalview / io / vcf / VCFLoaderTest.java

diff --git a/test/jalview/io/vcf/VCFLoaderTest.java b/test/jalview/io/vcf/VCFLoaderTest.java
index 4a254d2..5607b4b 100644 (file)
--- a/test/jalview/io/vcf/VCFLoaderTest.java
+++ b/test/jalview/io/vcf/VCFLoaderTest.java
@@ -55,7 +55,7 @@ public class VCFLoaderTest
 
   private static final String[] VCF = { "##fileformat=VCFv4.2",
       "##INFO=<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency, for each ALT allele, in the same order as listed\">",
-      "##reference=GRCh38",
+      "##reference=Homo_sapiens/GRCh38",
       "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO",
       // A/T,C variants in position 2 of gene sequence (precedes transcript)
       // should create 2 variant features with respective scores
@@ -191,7 +191,8 @@ public class VCFLoaderTest
     SequenceI gene1 = alignment.findName("gene1");
     int[] to = new int[] { 45051610, 45051634 };
     int[] from = new int[] { gene1.getStart(), gene1.getEnd() };
-    gene1.setGeneLoci("human", "GRCh38", "17", new MapList(from, to, 1, 1));
+    gene1.setGeneLoci("homo_sapiens", "GRCh38", "17", new MapList(from, to,
+            1, 1));
 
     /*
      * map 'transcript1' to chromosome via 'gene1'
@@ -201,7 +202,8 @@ public class VCFLoaderTest
     to = new int[] { 45051612, 45051619, 45051624, 45051633 };
     SequenceI transcript1 = alignment.findName("transcript1");
     from = new int[] { transcript1.getStart(), transcript1.getEnd() };
-    transcript1.setGeneLoci("human", "GRCh38", "17", new MapList(from, to,
+    transcript1.setGeneLoci("homo_sapiens", "GRCh38", "17", new MapList(
+            from, to,
             1, 1));
 
     /*
@@ -210,7 +212,8 @@ public class VCFLoaderTest
     SequenceI gene2 = alignment.findName("gene2");
     to = new int[] { 45051634, 45051610 };
     from = new int[] { gene2.getStart(), gene2.getEnd() };
-    gene2.setGeneLoci("human", "GRCh38", "17", new MapList(from, to, 1, 1));
+    gene2.setGeneLoci("homo_sapiens", "GRCh38", "17", new MapList(from, to,
+            1, 1));
 
     /*
      * map 'transcript2' to chromosome via 'gene2'
@@ -220,7 +223,8 @@ public class VCFLoaderTest
     to = new int[] { 45051633, 45051624, 45051619, 45051612 };
     SequenceI transcript2 = alignment.findName("transcript2");
     from = new int[] { transcript2.getStart(), transcript2.getEnd() };
-    transcript2.setGeneLoci("human", "GRCh38", "17", new MapList(from, to,
+    transcript2.setGeneLoci("homo_sapiens", "GRCh38", "17", new MapList(
+            from, to,
             1, 1));
 
     /*
@@ -248,7 +252,8 @@ public class VCFLoaderTest
     SequenceI gene3 = alignment.findName("gene3");
     to = new int[] { 45051610, 45051634 };
     from = new int[] { gene3.getStart(), gene3.getEnd() };
-    gene3.setGeneLoci("human", "GRCh38", "5", new MapList(from, to, 1, 1));
+    gene3.setGeneLoci("homo_sapiens", "GRCh38", "5", new MapList(from, to,
+            1, 1));
 
     /*
      * map 'transcript3' to chromosome
@@ -256,7 +261,8 @@ public class VCFLoaderTest
     SequenceI transcript3 = alignment.findName("transcript3");
     to = new int[] { 45051612, 45051619, 45051624, 45051633 };
     from = new int[] { transcript3.getStart(), transcript3.getEnd() };
-    transcript3.setGeneLoci("human", "GRCh38", "5", new MapList(from, to,
+    transcript3.setGeneLoci("homo_sapiens", "GRCh38", "5", new MapList(
+            from, to,
             1, 1));
 
     /*
@@ -266,7 +272,8 @@ public class VCFLoaderTest
     to = new int[] { 45051615, 45051617, 45051619, 45051632, 45051634,
         45051634 };
     from = new int[] { transcript4.getStart(), transcript4.getEnd() };
-    transcript4.setGeneLoci("human", "GRCh38", "5", new MapList(from, to,
+    transcript4.setGeneLoci("homo_sapiens", "GRCh38", "5", new MapList(
+            from, to,
             1, 1));
 
     /*