diff --git a/src/main/java/htsjdk/variant/vcf/VCFFilterHeaderLine.java b/src/main/java/htsjdk/variant/vcf/VCFFilterHeaderLine.java index 6c7186535..5130963ac 100644 --- a/src/main/java/htsjdk/variant/vcf/VCFFilterHeaderLine.java +++ b/src/main/java/htsjdk/variant/vcf/VCFFilterHeaderLine.java @@ -33,6 +33,8 @@ * 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 @@ -40,7 +42,7 @@ * @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); } @@ -48,7 +50,7 @@ public VCFFilterHeaderLine(String name, String 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); } @@ -58,7 +60,7 @@ 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")); } @@ -66,4 +68,12 @@ public VCFFilterHeaderLine(String line, VCFHeaderVersion version) { public boolean shouldBeAddedToDictionary() { return true; } -} \ No newline at end of file + + /** + * get the "Description" field + * @return the "Description" field + */ + public String getDescription() { + return getGenericFieldValue("Description"); + } +} diff --git a/src/test/java/htsjdk/variant/vcf/VCFHeaderUnitTest.java b/src/test/java/htsjdk/variant/vcf/VCFHeaderUnitTest.java index af875fcdc..e9135cc72 100644 --- a/src/test/java/htsjdk/variant/vcf/VCFHeaderUnitTest.java +++ b/src/test/java/htsjdk/variant/vcf/VCFHeaderUnitTest.java @@ -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");