...classes loaded when an indexed VCF file is parsed by Jalview
 htsjdk.samtools.AbstractSAMHeaderRecord
 htsjdk.samtools.Defaults
 htsjdk.samtools.FileTruncatedException
 htsjdk.samtools.SAMException
 htsjdk.samtools.SamFlagField
 htsjdk.samtools.SAMFormatException
 htsjdk.samtools.SAMSequenceDictionary
 htsjdk.samtools.SAMSequenceRecord
 htsjdk.samtools.seekablestream.ISeekableStreamFactory
 htsjdk.samtools.seekablestream.SeekableBufferedStream
 htsjdk.samtools.seekablestream.SeekableFileStream
 htsjdk.samtools.seekablestream.SeekableFTPStream
 htsjdk.samtools.seekablestream.SeekableHTTPStream
 htsjdk.samtools.seekablestream.SeekablePathStream
 htsjdk.samtools.seekablestream.SeekableStream
 htsjdk.samtools.seekablestream.SeekableStreamFactory
 htsjdk.samtools.util.AbstractIterator
 htsjdk.samtools.util.BlockCompressedFilePointerUtil
 htsjdk.samtools.util.BlockCompressedInputStream
 htsjdk.samtools.util.BlockGunzipper
 htsjdk.samtools.util.CloseableIterator
 htsjdk.samtools.util.CloserUtil
 htsjdk.samtools.util.CustomGzipOutputStream
 htsjdk.samtools.util.IOUtil
 htsjdk.samtools.util.IterableOnceIterator
 htsjdk.samtools.util.Locatable
 htsjdk.samtools.util.LocationAware
 htsjdk.samtools.util.Log
 htsjdk.samtools.util.Md5CalculatingOutputStream
 htsjdk.samtools.util.RuntimeIOException
 htsjdk.samtools.util.StringUtil
 htsjdk.samtools.util.zip.InflaterFactory
 htsjdk.tribble.AbstractFeatureCodec
 htsjdk.tribble.AbstractFeatureReader
 htsjdk.tribble.AsciiFeatureCodec
 htsjdk.tribble.CloseableTribbleIterator
 htsjdk.tribble.Feature
 htsjdk.tribble.FeatureCodec
 htsjdk.tribble.FeatureCodecHeader
 htsjdk.tribble.FeatureReader
 htsjdk.tribble.NameAwareCodec
 htsjdk.tribble.readers.LineIterator
 htsjdk.tribble.readers.LineIteratorImpl
 htsjdk.tribble.readers.LineReader
 htsjdk.tribble.readers.LongLineBufferedReader
 htsjdk.tribble.readers.Positional
 htsjdk.tribble.readers.PositionalBufferedStream
 htsjdk.tribble.readers.SynchronousLineReader
 htsjdk.tribble.readers.TabixIteratorLineReader
 htsjdk.tribble.readers.TabixReader
 htsjdk.tribble.TabixFeatureReader
 htsjdk.tribble.TribbleException
 htsjdk.tribble.TribbleIndexedFeatureReader
 htsjdk.tribble.util.ParsingUtils
 htsjdk.tribble.util.RemoteURLHelper
 htsjdk.tribble.util.URLHelper
 htsjdk.variant.variantcontext.Allele
 htsjdk.variant.variantcontext.CommonInfo
 htsjdk.variant.variantcontext.GenotypesContext
 htsjdk.variant.variantcontext.LazyGenotypesContext
 htsjdk.variant.variantcontext.VariantContext
 htsjdk.variant.variantcontext.VariantContextBuilder
 htsjdk.variant.vcf.AbstractVCFCodec
 htsjdk.variant.vcf.VCF3Parser
 htsjdk.variant.vcf.VCF4Parser
 htsjdk.variant.vcf.VCFCodec
 htsjdk.variant.vcf.VCFCompoundHeaderLine
 htsjdk.variant.vcf.VCFContigHeaderLine
 htsjdk.variant.vcf.VCFFileReader
 htsjdk.variant.vcf.VCFFilterHeaderLine
 htsjdk.variant.vcf.VCFFormatHeaderLine
 htsjdk.variant.vcf.VCFHeader
 htsjdk.variant.vcf.VCFHeaderLine
 htsjdk.variant.vcf.VCFHeaderLineCount
 htsjdk.variant.vcf.VCFHeaderLineTranslator
 htsjdk.variant.vcf.VCFHeaderLineType
 htsjdk.variant.vcf.VCFHeaderVersion
 htsjdk.variant.vcf.VCFIDHeaderLine
 htsjdk.variant.vcf.VCFInfoHeaderLine
 htsjdk.variant.vcf.VCFLineParser // not in src
 htsjdk.variant.vcf.VCFSimpleHeaderLine
 htsjdk.variant.vcf.VCFStandardHeaderLines