Merge branch 'develop' into ben/gecos_colour_schemes

[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 16ff41b..176b21d 100644 (file)
--- a/src/jalview/ext/htsjdk/VCFReader.java
+++ b/src/jalview/ext/htsjdk/VCFReader.java
@@ -20,8 +20,6 @@
  */
 package jalview.ext.htsjdk;
 
-import jalview.bin.Cache;
-
 import java.io.Closeable;
 import java.io.File;
 import java.io.IOException;
@@ -30,6 +28,7 @@ import htsjdk.samtools.util.CloseableIterator;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.vcf.VCFFileReader;
 import htsjdk.variant.vcf.VCFHeader;
+import jalview.bin.Console;
 
 /**
  * A thin wrapper for htsjdk classes to read either plain, or compressed, or
@@ -48,10 +47,12 @@ public class VCFReader implements Closeable, Iterable<VariantContext>
   private VCFFileReader reader;
 
   /**
-   * Constructor given a raw or compressed VCF file or a (csi or tabix) index file
+   * Constructor given a raw or compressed VCF file or a (csi or tabix) index
+   * file
    * <p>
-   * If the file path ends in ".tbi" or ".csi", <em>or</em> appending one of these
-   * extensions gives a valid file path, open as indexed, else as unindexed.
+   * If the file path ends in ".tbi" or ".csi", <em>or</em> appending one of
+   * these extensions gives a valid file path, open as indexed, else as
+   * unindexed.
    * 
    * @param f
    * @throws IOException
@@ -85,7 +86,7 @@ public class VCFReader implements Closeable, Iterable<VariantContext>
     }
     else
     {
-      Cache.log.error("File not found: " + filePath);
+      Console.error("File not found: " + filePath);
     }
   }
 
@@ -154,7 +155,7 @@ public class VCFReader implements Closeable, Iterable<VariantContext>
           final String chrom, final int start, final int end)
   {
     final CloseableIterator<VariantContext> it = reader.iterator();
-    
+
     return new CloseableIterator<VariantContext>()
     {
       boolean atEnd = false;