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
{
final CloseableIterator<VariantContext> it = reader.iterator();
- return new CloseableIterator<VariantContext>()
+ return new CloseableIterator()
{
boolean atEnd = false;
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;