diff --git a/src/java/htsjdk/variant/vcf/VCFCompoundHeaderLine.java b/src/java/htsjdk/variant/vcf/VCFCompoundHeaderLine.java
index 1a2d773612..48e0cdf0db 100644
--- a/src/java/htsjdk/variant/vcf/VCFCompoundHeaderLine.java
+++ b/src/java/htsjdk/variant/vcf/VCFCompoundHeaderLine.java
@@ -249,16 +249,34 @@ protected String toStringEncoding() {
}
/**
- * returns true if we're equal to another compounder header line
+ * returns true if we're equal to another compound header line
* @param o a compound header line
* @return true if equal
*/
- public boolean equals(Object o) {
- if (!(o instanceof VCFCompoundHeaderLine))
+ @Override
+ public boolean equals(final Object o) {
+ if ( this == o ) {
+ return true;
+ }
+ if ( o == null || getClass() != o.getClass() || ! super.equals(o) ) {
return false;
- VCFCompoundHeaderLine other = (VCFCompoundHeaderLine) o;
- return equalsExcludingDescription(other) &&
- description.equals(other.description);
+ }
+
+ final VCFCompoundHeaderLine that = (VCFCompoundHeaderLine) o;
+ return equalsExcludingDescription(that) &&
+ description.equals(that.description);
+ }
+
+ @Override
+ public int hashCode() {
+ int result = super.hashCode();
+ result = 31 * result + name.hashCode();
+ result = 31 * result + count;
+ result = 31 * result + (countType != null ? countType.hashCode() : 0); // only nullable field according to validate()
+ result = 31 * result + description.hashCode();
+ result = 31 * result + type.hashCode();
+ result = 31 * result + lineType.hashCode();
+ return result;
}
public boolean equalsExcludingDescription(VCFCompoundHeaderLine other) {
diff --git a/src/java/htsjdk/variant/vcf/VCFContigHeaderLine.java b/src/java/htsjdk/variant/vcf/VCFContigHeaderLine.java
index 64c5d7f8f5..12e400c95c 100644
--- a/src/java/htsjdk/variant/vcf/VCFContigHeaderLine.java
+++ b/src/java/htsjdk/variant/vcf/VCFContigHeaderLine.java
@@ -34,6 +34,8 @@
/**
* A special class representing a contig VCF header line. Knows the true contig order and sorts on that
*
+ * Note: this class has a natural ordering that is inconsistent with equals()
+ *
* @author mdepristo
*/
public class VCFContigHeaderLine extends VCFSimpleHeaderLine {
@@ -82,6 +84,26 @@ public SAMSequenceRecord getSAMSequenceRecord() {
return record;
}
+ @Override
+ public boolean equals(final Object o) {
+ if ( this == o ) {
+ return true;
+ }
+ if ( o == null || getClass() != o.getClass() || ! super.equals(o) ) {
+ return false;
+ }
+
+ final VCFContigHeaderLine that = (VCFContigHeaderLine) o;
+ return contigIndex.equals(that.contigIndex);
+ }
+
+ @Override
+ public int hashCode() {
+ int result = super.hashCode();
+ result = 31 * result + contigIndex.hashCode();
+ return result;
+ }
+
/**
* IT IS CRITICAL THAT THIS BE OVERRIDDEN SO WE SORT THE CONTIGS IN THE CORRECT ORDER
*/
diff --git a/src/java/htsjdk/variant/vcf/VCFHeader.java b/src/java/htsjdk/variant/vcf/VCFHeader.java
index f763729885..f0c432b3a0 100644
--- a/src/java/htsjdk/variant/vcf/VCFHeader.java
+++ b/src/java/htsjdk/variant/vcf/VCFHeader.java
@@ -32,6 +32,7 @@
import htsjdk.variant.utils.GeneralUtils;
import htsjdk.variant.variantcontext.VariantContextComparator;
+import java.io.Serializable;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
@@ -57,7 +58,8 @@
*
* A class representing the VCF header
*/
-public class VCFHeader {
+public class VCFHeader implements Serializable {
+ public static final long serialVersionUID = 1L;
// the mandatory header fields
public enum HEADER_FIELDS {
diff --git a/src/java/htsjdk/variant/vcf/VCFHeaderLine.java b/src/java/htsjdk/variant/vcf/VCFHeaderLine.java
index 284f0d4520..00d0f45f0f 100644
--- a/src/java/htsjdk/variant/vcf/VCFHeaderLine.java
+++ b/src/java/htsjdk/variant/vcf/VCFHeaderLine.java
@@ -27,6 +27,7 @@
import htsjdk.tribble.TribbleException;
+import java.io.Serializable;
import java.util.Map;
@@ -37,7 +38,9 @@
*
* A class representing a key=value entry in the VCF header
*/
-public class VCFHeaderLine implements Comparable {
+public class VCFHeaderLine implements Comparable, Serializable {
+ public static final long serialVersionUID = 1L;
+
protected static final boolean ALLOW_UNBOUND_DESCRIPTIONS = true;
protected static final String UNBOUND_DESCRIPTION = "Not provided in original VCF header";
@@ -101,10 +104,25 @@ protected String toStringEncoding() {
return mKey + "=" + mValue;
}
- public boolean equals(Object o) {
- if ( !(o instanceof VCFHeaderLine) )
+ @Override
+ public boolean equals(final Object o) {
+ if ( this == o ) {
+ return true;
+ }
+ if ( o == null || getClass() != o.getClass() ) {
return false;
- return mKey.equals(((VCFHeaderLine)o).getKey()) && mValue.equals(((VCFHeaderLine)o).getValue());
+ }
+
+ final VCFHeaderLine that = (VCFHeaderLine) o;
+ return mKey.equals(that.mKey) && // key not nullable
+ (mValue != null ? mValue.equals(that.mValue) : that.mValue == null); // value is nullable
+ }
+
+ @Override
+ public int hashCode() {
+ int result = mKey.hashCode();
+ result = 31 * result + (mValue != null ? mValue.hashCode() : 0);
+ return result;
}
public int compareTo(Object other) {
diff --git a/src/java/htsjdk/variant/vcf/VCFSimpleHeaderLine.java b/src/java/htsjdk/variant/vcf/VCFSimpleHeaderLine.java
index 16e90e3409..3401d08315 100644
--- a/src/java/htsjdk/variant/vcf/VCFSimpleHeaderLine.java
+++ b/src/java/htsjdk/variant/vcf/VCFSimpleHeaderLine.java
@@ -98,18 +98,26 @@ protected String toStringEncoding() {
return getKey() + "=" + VCFHeaderLine.toStringEncoding(map);
}
- public boolean equals(Object o) {
- if ( !(o instanceof VCFSimpleHeaderLine) )
- return false;
- VCFSimpleHeaderLine other = (VCFSimpleHeaderLine)o;
- if ( !name.equals(other.name) || genericFields.size() != other.genericFields.size() )
+ @Override
+ public boolean equals( final Object o ) {
+ if ( this == o ) {
+ return true;
+ }
+ if ( o == null || getClass() != o.getClass() || ! super.equals(o) ) {
return false;
- for ( Map.Entry entry : genericFields.entrySet() ) {
- if ( !entry.getValue().equals(other.genericFields.get(entry.getKey())) )
- return false;
}
-
- return true;
+
+ final VCFSimpleHeaderLine that = (VCFSimpleHeaderLine) o;
+ return name.equals(that.name) &&
+ genericFields.equals(that.genericFields);
+ }
+
+ @Override
+ public int hashCode() {
+ int result = super.hashCode();
+ result = 31 * result + name.hashCode();
+ result = 31 * result + genericFields.hashCode();
+ return result;
}
public String getID() {
diff --git a/src/tests/java/htsjdk/variant/vcf/VCFHeaderUnitTest.java b/src/tests/java/htsjdk/variant/vcf/VCFHeaderUnitTest.java
index 339d203284..bc97b918c7 100644
--- a/src/tests/java/htsjdk/variant/vcf/VCFHeaderUnitTest.java
+++ b/src/tests/java/htsjdk/variant/vcf/VCFHeaderUnitTest.java
@@ -38,11 +38,15 @@
import org.testng.Assert;
import org.testng.annotations.Test;
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
import java.io.PrintWriter;
import java.io.StringReader;
import java.math.BigInteger;
@@ -51,6 +55,7 @@
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
+import java.util.Set;
/**
* Created by IntelliJ IDEA.
@@ -192,6 +197,35 @@ public void testVCFHeaderAddDuplicateHeaderLine() {
Assert.assertEquals(numHeaderLinesBefore, numHeaderLinesAfter);
}
+ @Test
+ public void testVCFHeaderSerialization() throws Exception {
+ final VCFFileReader reader = new VCFFileReader(new File("testdata/htsjdk/variant/HiSeq.10000.vcf"), false);
+ final VCFHeader originalHeader = reader.getFileHeader();
+ reader.close();
+
+ final ByteArrayOutputStream byteArrayStream = new ByteArrayOutputStream();
+ final ObjectOutputStream out = new ObjectOutputStream(byteArrayStream);
+ out.writeObject(originalHeader);
+ out.close();
+
+ final ObjectInputStream in = new ObjectInputStream(new ByteArrayInputStream(byteArrayStream.toByteArray()));
+ final VCFHeader deserializedHeader = (VCFHeader)in.readObject();
+ in.close();
+
+ Assert.assertEquals(deserializedHeader.getMetaDataInInputOrder(), originalHeader.getMetaDataInInputOrder(), "Header metadata does not match before/after serialization");
+ Assert.assertEquals(deserializedHeader.getContigLines(), originalHeader.getContigLines(), "Contig header lines do not match before/after serialization");
+ Assert.assertEquals(deserializedHeader.getFilterLines(), originalHeader.getFilterLines(), "Filter header lines do not match before/after serialization");
+ Assert.assertEquals(deserializedHeader.getFormatHeaderLines(), originalHeader.getFormatHeaderLines(), "Format header lines do not match before/after serialization");
+ Assert.assertEquals(deserializedHeader.getIDHeaderLines(), originalHeader.getIDHeaderLines(), "ID header lines do not match before/after serialization");
+ Assert.assertEquals(deserializedHeader.getInfoHeaderLines(), originalHeader.getInfoHeaderLines(), "Info header lines do not match before/after serialization");
+ Assert.assertEquals(deserializedHeader.getOtherHeaderLines(), originalHeader.getOtherHeaderLines(), "Other header lines do not match before/after serialization");
+ Assert.assertEquals(deserializedHeader.getGenotypeSamples(), originalHeader.getGenotypeSamples(), "Genotype samples not the same before/after serialization");
+ Assert.assertEquals(deserializedHeader.samplesWereAlreadySorted(), originalHeader.samplesWereAlreadySorted(), "Sortedness of samples not the same before/after serialization");
+ Assert.assertEquals(deserializedHeader.getSampleNamesInOrder(), originalHeader.getSampleNamesInOrder(), "Sorted list of sample names in header not the same before/after serialization");
+ Assert.assertEquals(deserializedHeader.getSampleNameToOffset(), originalHeader.getSampleNameToOffset(), "Sample name to offset map not the same before/after serialization");
+ Assert.assertEquals(deserializedHeader.toString(), originalHeader.toString(), "String representation of header not the same before/after serialization");
+ }
+
/**
* a little utility function for all tests to md5sum a file
* Shameless taken from: