package jalview.ext.htsjdk;
-import htsjdk.samtools.util.CloseableIterator;
-import htsjdk.variant.variantcontext.VariantContext;
-import htsjdk.variant.vcf.VCFFileReader;
-import htsjdk.variant.vcf.VCFHeader;
+import jalview.bin.Cache;
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;
+
/**
* A thin wrapper for htsjdk classes to read either plain, or compressed, or
* compressed and indexed VCF files
private static final String TBI_EXTENSION = ".tbi";
+ private static final String CSI_EXTENSION = ".csi";
+
private boolean indexed;
private VCFFileReader reader;
/**
- * Constructor given a raw or compressed VCF file or a (tabix) index file
+ * Constructor given a raw or compressed VCF file or a (csi or tabix) index file
* <p>
- * For now, file type is inferred from its suffix: .gz or .bgz for compressed
- * data, .tbi for an index file, anything else is assumed to be plain text
- * VCF.
+ * 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
*/
public VCFReader(String filePath) throws IOException
{
- if (filePath.endsWith(GZ))
+ indexed = false;
+ if (filePath.endsWith(TBI_EXTENSION)
+ || filePath.endsWith(CSI_EXTENSION))
{
- if (new File(filePath + TBI_EXTENSION).exists())
- {
- indexed = true;
- }
+ indexed = true;
+ filePath = filePath.substring(0, filePath.length() - 4);
}
- else if (filePath.endsWith(TBI_EXTENSION))
+ else if (new File(filePath + TBI_EXTENSION).exists())
+ {
+ indexed = true;
+ }
+ else if (new File(filePath + CSI_EXTENSION).exists())
{
indexed = true;
- filePath = filePath.substring(0, filePath.length() - 4);
}
- reader = new VCFFileReader(new File(filePath), indexed);
+ /*
+ * we pass the name of the unindexed file to htsjdk,
+ * with a flag to assert whether it is indexed
+ */
+ File file = new File(filePath);
+ if (file.exists())
+ {
+ reader = new VCFFileReader(file, indexed);
+ }
+ else
+ {
+ Cache.log.error("File not found: " + filePath);
+ }
}
@Override
public CloseableIterator<VariantContext> query(final String chrom,
final int start, final int end)
{
- if (reader == null) {
- return null;
- }
+ if (reader == null)
+ {
+ return null;
+ }
if (indexed)
{
return reader.query(chrom, start, end);
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;