SamSequenceRecord implements Locatable (#1459)

* Make SamSequenceRecord implement Locatable so it can be used with overlaps checks and in utilities that use locatable.

Author: lindenb

src/main/java/htsjdk/samtools/SAMSequenceRecord.java

@@ -24,22 +24,20 @@
 package htsjdk.samtools;
 
 
-import htsjdk.variant.variantcontext.VariantContext;
 
 import java.math.BigInteger;
-import java.net.URI;
-import java.net.URISyntaxException;
 import java.util.Arrays;
 import java.util.HashSet;
 import java.util.Map;
 import java.util.Set;
 import java.util.regex.Pattern;
+import htsjdk.samtools.util.Locatable;
 
 /**
  * Header information about a reference sequence.  Corresponds to @SQ header record in SAM text header.
  */
 
-public class SAMSequenceRecord extends AbstractSAMHeaderRecord implements Cloneable
+public class SAMSequenceRecord extends AbstractSAMHeaderRecord implements Cloneable, Locatable
 {
     public static final long serialVersionUID = 1L; // AbstractSAMHeaderRecord implements Serializable
     public final static int UNAVAILABLE_SEQUENCE_INDEX = -1;
@@ -228,5 +226,26 @@ public String toString() {
     public String getSAMString() {
         return new SAMTextHeaderCodec().getSQLine(this);
     }
+    /** always returns <code>getSequenceName()</code> 
+     * @see #getSequenceName()
+     * */
+    @Override
+    public final String getContig() {
+        return this.getSequenceName();
+    }
+    
+    /** always returns 1 */
+    @Override
+    public final int getStart() {
+        return 1;
+    }
+    
+    /** always returns <code>getSequenceLength()</code> 
+     * @see #getSequenceLength()
+     * */
+    @Override
+    public final int getEnd() {
+        return this.getSequenceLength();
+    }
 }
 

src/test/java/htsjdk/samtools/SAMSequenceRecordTest.java

@@ -24,6 +24,7 @@
 package htsjdk.samtools;
 
 import htsjdk.HtsjdkTest;
+import htsjdk.samtools.util.Interval;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
@@ -44,6 +45,17 @@ public void testGetSAMString() {
         Assert.assertEquals("@SQ\tSN:chr5_but_without_a_prefix\tLN:271828\tSP:Psephophorus terrypratchetti\tAS:GRCt01\tM5:7a6dd3d307de916b477e7bf304ac22bc", r.getSAMString());
     }
 
+    @Test
+    public void testLocatable() {
+        final SAMSequenceRecord r = new SAMSequenceRecord("1", 100);
+        Assert.assertTrue(r.overlaps(r));
+        Assert.assertEquals(r.getStart(),1);
+        Assert.assertEquals(r.getEnd(),r.getSequenceLength());
+        Assert.assertEquals(r.getLengthOnReference(),r.getSequenceLength());
+        Assert.assertTrue(r.overlaps(new Interval(r.getContig(), 50, 150)));
+        Assert.assertFalse(r.overlaps(new Interval(r.getContig(), 101, 101)));
+    }
+    
     @DataProvider
     public Object[][] testIsSameSequenceData() {
         final SAMSequenceRecord rec1 = new SAMSequenceRecord("chr1", 100);