Make VCFHeader not throw exception if contig header lines lack length…

… field

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

@@ -76,9 +76,14 @@ public Integer getContigIndex() {
         return contigIndex;
     }
 
+    /**
+     * Get the SAMSequenceRecord that corresponds to this VCF header line.
+     * @return The SAMSequenceRecord containing the ID, length, assembly, and index of this contig. Returns null if the
+     * contig header line does not have a length.
+     */
 	public SAMSequenceRecord getSAMSequenceRecord() {
 		final String lengthString = this.getGenericFieldValue("length");
-		if (lengthString == null) throw new TribbleException("Contig " + this.getID() + " does not have a length field.");
+		if (lengthString == null) return null;
 		final SAMSequenceRecord record = new SAMSequenceRecord(this.getID(), Integer.parseInt(lengthString));
         record.setAssembly(this.getGenericFieldValue("assembly"));
 		record.setSequenceIndex(this.contigIndex);

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

@@ -261,7 +261,7 @@ public List<VCFContigHeaderLine> getContigLines() {
 
     /**
      * Returns the contigs in this VCF file as a SAMSequenceDictionary. Returns null if contigs lines are
-     * not present in the header. Throws SAMException if one or more contig lines do not have length
+     * not present in the header. Returns null if one or more contig lines do not have length
      * information.
      */
     public SAMSequenceDictionary getSequenceDictionary() {
@@ -270,7 +270,9 @@ public SAMSequenceDictionary getSequenceDictionary() {
 
         final List<SAMSequenceRecord> sequenceRecords = new ArrayList<SAMSequenceRecord>(contigHeaderLines.size());
         for (final VCFContigHeaderLine contigHeaderLine : contigHeaderLines) {
-            sequenceRecords.add(contigHeaderLine.getSAMSequenceRecord());
+            final SAMSequenceRecord samSequenceRecord = contigHeaderLine.getSAMSequenceRecord();
+            if (samSequenceRecord == null) return null;
+            sequenceRecords.add(samSequenceRecord);
         }
 
         return new SAMSequenceDictionary(sequenceRecords);

src/test/java/htsjdk/variant/vcf/VCFHeaderUnitTest.java

@@ -239,6 +239,18 @@ public void testVCFHeaderAddContigLine() {
     }
 
     @Test
+    public void testVCFHeaderContigLineMissingLength() {
+        final VCFHeader header = getHiSeqVCFHeader();
+        final VCFContigHeaderLine contigLine = new VCFContigHeaderLine(
+                "<ID=chr1>", VCFHeaderVersion.VCF4_0, VCFHeader.CONTIG_KEY, 0);
+        header.addMetaDataLine(contigLine);
+        Assert.assertTrue(header.getContigLines().contains(contigLine), "Test contig line not found in contig header lines");
+        Assert.assertTrue(header.getMetaDataInInputOrder().contains(contigLine), "Test contig line not found in set of all header lines");
+
+        Assert.assertNull(header.getSequenceDictionary());
+    }
+
+        @Test
     public void testVCFHeaderHonorContigLineOrder() throws IOException {
         try (final VCFFileReader vcfReader = new VCFFileReader(new File(variantTestDataRoot + "dbsnp_135.b37.1000.vcf"), false)) {
             // start with a header with a bunch of contig lines