Added getDescription() in VCFFilterHeaderLine #726

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merged 2 commits into from Nov 22, 2016
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@@ -33,22 +33,24 @@
* A class representing a key=value entry for FILTER fields in the VCF header
*/
public class VCFFilterHeaderLine extends VCFSimpleHeaderLine {
+
+ private static final long serialVersionUID = 1L;
/**
* create a VCF filter header line
*
* @param name the name for this header line
* @param description the description for this header line
*/
- public VCFFilterHeaderLine(String name, String description) {
+ public VCFFilterHeaderLine(final String name, final String description) {
super("FILTER", name, description);
}
/**
* Convenience constructor for FILTER whose description is the name
* @param name
*/
- public VCFFilterHeaderLine(String name) {
+ public VCFFilterHeaderLine(final String name) {
super("FILTER", name, name);
}
@@ -58,12 +60,20 @@ public VCFFilterHeaderLine(String name) {
* @param line the header line
* @param version the vcf header version
*/
- public VCFFilterHeaderLine(String line, VCFHeaderVersion version) {
+ public VCFFilterHeaderLine(final String line, final VCFHeaderVersion version) {
super(line, version, "FILTER", Arrays.asList("ID", "Description"));
}
@Override
public boolean shouldBeAddedToDictionary() {
return true;
}
-}
+
+ /**
+ * get the "Description" field
+ * @return the "Description" field
+ */
+ public String getDescription() {
+ return getGenericFieldValue("Description");
+ }
+}
@@ -196,7 +196,9 @@ public void testVCFHeaderAddFormatLine() {
@Test
public void testVCFHeaderAddFilterLine() {
final VCFHeader header = getHiSeqVCFHeader();
- final VCFFilterHeaderLine filterLine = new VCFFilterHeaderLine("TestFilterLine");
+ final String filterDesc = "TestFilterLine Description";
+ final VCFFilterHeaderLine filterLine = new VCFFilterHeaderLine("TestFilterLine",filterDesc);
+ Assert.assertEquals(filterDesc,filterLine.getDescription());
header.addMetaDataLine(filterLine);
Assert.assertTrue(header.getFilterLines().contains(filterLine), "TestFilterLine not found in filter header lines");