Ignore version validation for BCF in VCFHeaderReader because we only need the header

src/main/java/htsjdk/variant/utils/SAMSequenceDictionaryExtractor.java

@@ -29,9 +29,10 @@
 import htsjdk.samtools.cram.structure.Container;
 import htsjdk.samtools.cram.structure.CramHeader;
 import htsjdk.samtools.reference.ReferenceSequenceFileFactory;
+import htsjdk.samtools.seekablestream.SeekablePathStream;
+import htsjdk.samtools.seekablestream.SeekableStream;
 import htsjdk.samtools.util.*;
 import htsjdk.tribble.util.ParsingUtils;
-import htsjdk.variant.vcf.VCFFileReader;
 
 import java.io.File;
 import java.io.IOException;
@@ -102,8 +103,10 @@ SAMSequenceDictionary extractDictionary(final Path sam) {
 
             @Override
             SAMSequenceDictionary extractDictionary(final Path vcf) {
-                try (VCFFileReader vcfPathReader = new VCFFileReader(vcf, false)){
-                    return vcfPathReader.getFileHeader().getSequenceDictionary();
+                try (SeekableStream vcfSeekableStream = new SeekablePathStream(vcf)){
+                    return VCFHeaderReader.readHeaderFrom(vcfSeekableStream).getSequenceDictionary();
+                } catch (IOException e) {
+                    throw new RuntimeIOException(e);
                 }
             }
         },

src/main/java/htsjdk/variant/utils/VCFHeaderReader.java

@@ -1,6 +1,5 @@
 package htsjdk.variant.utils;
 
-import htsjdk.samtools.SamStreams;
 import htsjdk.samtools.cram.io.InputStreamUtils;
 import htsjdk.samtools.seekablestream.SeekableStream;
 import htsjdk.samtools.util.IOUtil;
@@ -30,6 +29,7 @@ private VCFHeaderReader(){}
      * Read a VCF header from a stream that may be a VCF file (possibly gzip or block compressed) or a BCF file.
      * After successfully reading a header the stream is positioned immediately after the header, otherwise, if an
      * exception is thrown, the state of the stream is undefined.
+     * For BCF files, the version validation is ignored
      *
      * @param in the stream to read the header from
      * @return the VCF header read from the stream
@@ -43,7 +43,12 @@ public static VCFHeader readHeaderFrom(final SeekableStream in) throws IOExcepti
         if (magicBytes[0] == '#') { // VCF
             return readHeaderFrom(in, new VCFCodec());
         } else if (Arrays.equals(magicBytes, BCFVersion.MAGIC_HEADER_START)) {
-            return readHeaderFrom(in, new BCF2Codec());
+            return readHeaderFrom(in, new BCF2Codec() {
+                @Override
+                protected void validateVersionCompatibility(final BCFVersion supportedVersion, final BCFVersion actualVersion) {
+                   // ignore validation, might be used to get samples in recent BCF
+                }
+            });
         }
         throw new TribbleException.InvalidHeader("No VCF header found in " + in.getSource());
     }

src/test/java/htsjdk/variant/utils/SAMSequenceDictionaryExtractorTest.java

@@ -46,6 +46,7 @@ public Object[][] dictionaries() {
                 new Object[]{"test1_comp.interval_list", "test1.dict"},
                 new Object[]{"test1.vcf", "test1.dict"},
                 new Object[]{"test1.dict", "test1.dict"},
+                new Object[]{"test1.bcf2_2.bcf", "test1.dict"},
                 new Object[]{"empty.interval_list", "test1.dict"},
                 new Object[]{"Homo_sapiens_assembly18.trimmed.fasta", "Homo_sapiens_assembly18.trimmed.dict"},
                 new Object[]{"test2_comp.interval_list", "Homo_sapiens_assembly18.trimmed.dict"},

src/test/java/htsjdk/variant/utils/VCFHeaderReaderTest.java

@@ -22,6 +22,7 @@ Object[][] pathsData() {
                 {TEST_DATA_DIR + "VcfThatLacksAnIndex.vcf"},
                 {TEST_DATA_DIR + "VcfThatLacksAnIndex.vcf.bgz"},
                 {TEST_DATA_DIR + "VcfThatLacksAnIndex.vcf.gz"},
+                {TEST_DATA_DIR + "BCFVersion22Uncompressed.bcf"}
         };
     }