new interface VCFReader (#1473)

* Added a new VCFReader interface that VCFFileReader implements.

src/main/java/htsjdk/variant/vcf/VCFFileReader.java

@@ -24,21 +24,18 @@
 
 package htsjdk.variant.vcf;
 
-import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.samtools.util.CloseableIterator;
 import htsjdk.samtools.util.FileExtensions;
 import htsjdk.samtools.util.Interval;
 import htsjdk.samtools.util.IntervalList;
-import htsjdk.samtools.util.Locatable;
 import htsjdk.tribble.AbstractFeatureReader;
 import htsjdk.tribble.FeatureCodec;
 import htsjdk.tribble.FeatureReader;
 import htsjdk.tribble.TribbleException;
 import htsjdk.variant.bcf2.BCF2Codec;
 import htsjdk.variant.variantcontext.VariantContext;
 
-import java.io.Closeable;
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.Path;
@@ -48,7 +45,7 @@
 /**
  * Simplified interface for reading from VCF/BCF files.
  */
-public class VCFFileReader implements Closeable, Iterable<VariantContext> {
+public class VCFFileReader implements VCFReader {
 
     private final FeatureReader<VariantContext> reader;
 
@@ -311,9 +308,17 @@ public static Iterator<Interval> toIntervals(final VCFFileReader vcf, final bool
     /**
      * Returns the VCFHeader associated with this VCF/BCF file.
      */
-    public VCFHeader getFileHeader() {
+    @Override
+    public VCFHeader getHeader() {
         return (VCFHeader) reader.getHeader();
     }
+
+    /**
+     * Synonym of {@link #getHeader()}
+     */
+    public final VCFHeader getFileHeader() {
+        return getHeader();
+    }
 
     /**
      * Returns an iterator over all records in this VCF/BCF file.
@@ -344,16 +349,6 @@ public CloseableIterator<VariantContext> query(final String chrom, final int sta
         }
     }
 
-    /**
-     * Queries for records overlapping the {@link Locatable} specified.
-     * Note that this method requires VCF files with an associated index.  If no index exists a TribbleException will be thrown.
-     *
-     * @return non-null iterator over VariantContexts
-     */
-    public CloseableIterator<VariantContext> query(final Locatable locatable) {
-        return query(locatable.getContig(), locatable.getStart(), locatable.getEnd());
-    }
-
     @Override
     public void close() {
         try {
@@ -369,6 +364,7 @@ public void close() {
      *
      * @return true if the reader can be queried, i.e. if the underlying Tribble reader is queryable.
      */
+    @Override
     public boolean isQueryable() {
         return reader.isQueryable();
     }

src/main/java/htsjdk/variant/vcf/VCFReader.java

@@ -0,0 +1,74 @@
+/*
+ * The MIT License
+ *
+ * Copyright (c) 2013 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+
+package htsjdk.variant.vcf;
+
+import java.io.Closeable;
+import htsjdk.samtools.util.CloseableIterator;
+import htsjdk.samtools.util.Locatable;
+import htsjdk.variant.variantcontext.VariantContext;
+
+/**
+ * Interface for reading VCF/BCF files.
+ */
+public interface VCFReader extends Closeable, Iterable<VariantContext> {
+
+    /**
+     * Returns the VCFHeader associated with this VCFReader.
+     */
+    public VCFHeader getHeader();
+
+    /**
+     * Queries for records overlapping the region specified.
+     * Note that this method requires VCF files with an associated index.  If no index exists a TribbleException will be thrown.
+     *
+     * @param chrom the chomosome to query
+     * @param start query interval start
+     * @param end   query interval end
+     * @return non-null iterator over VariantContexts
+     */
+    public CloseableIterator<VariantContext> query(final String chrom, final int start, final int end);
+
+    /**
+     * Queries for records overlapping the {@link Locatable} specified.
+     * Note that this method requires VCF files with an associated index.  If no index exists a TribbleException will be thrown.
+     *
+     * @return non-null iterator over VariantContexts
+     */
+    public default CloseableIterator<VariantContext> query(final Locatable locatable) {
+        return query(locatable.getContig(), locatable.getStart(), locatable.getEnd());
+    }
+
+    /**
+     * A method to check if the reader is query-able, i.e. if a call to {@link VCFFileReader#query(String, int, int)}
+     * can be successful
+     *
+     * @return true if the reader can be queried, i.e. if the underlying Tribble reader is queryable.
+     */
+    public boolean isQueryable();
+
+    @Override
+    public CloseableIterator<VariantContext> iterator();
+
+}