JAL-3210 Barebones gradle/buildship/eclipse. See README

[jalview.git] / src / jalview / ext / htsjdk / VCFReader.java

diff --git a/src/jalview/ext/htsjdk/VCFReader.java b/src/jalview/ext/htsjdk/VCFReader.java
index 14c057f..04525f0 100644 (file)
--- a/src/jalview/ext/htsjdk/VCFReader.java
+++ b/src/jalview/ext/htsjdk/VCFReader.java
@@ -1,14 +1,14 @@
 package jalview.ext.htsjdk;
 
+import java.io.Closeable;
+import java.io.File;
+import java.io.IOException;
+
 import htsjdk.samtools.util.CloseableIterator;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.vcf.VCFFileReader;
 import htsjdk.variant.vcf.VCFHeader;
 
-import java.io.Closeable;
-import java.io.File;
-import java.io.IOException;
-
 /**
  * A thin wrapper for htsjdk classes to read either plain, or compressed, or
  * compressed and indexed VCF files
@@ -116,7 +116,7 @@ public class VCFReader implements Closeable, Iterable<VariantContext>
   {
     final CloseableIterator<VariantContext> it = reader.iterator();
     
-    return new CloseableIterator<VariantContext>()
+    return new CloseableIterator()
     {
       boolean atEnd = false;
 
@@ -145,7 +145,7 @@ public class VCFReader implements Closeable, Iterable<VariantContext>
           int vend = variant.getEnd();
           // todo what is the undeprecated way to get
           // the chromosome for the variant?
-          if (chrom.equals(variant.getChr()) && (vstart <= end)
+          if (chrom.equals(variant.getContig()) && (vstart <= end)
                   && (vend >= start))
           {
             return variant;