Type Members

1.  class BigVCFDatasource extends BigFileDatasource with DataSourceRegister
2.  class ComDatabricksBigVCFDatasource extends BigVCFDatasource with ComDatabricksDataSource
3.  class ComDatabricksVCFFileFormat extends VCFFileFormat with ComDatabricksDataSource
4.  class FilterContig extends AnyRef

   An extended Contig class used by filter parser that keeps an Option(contigName) updated under And and Or operations and provides other required functionalities

5.  class FilterInterval extends AnyRef

   An extended 1-based Interval class used by filter parser that keeps an Option(SimpleInterval) updated under And and Or operations and provides other required functionalities [Note: SimpleInterval class is org.broadinstitute.hellbender.utils.SimpleInterval]

6.  class InternalRowToVariantContextConverter extends GlowLogging with HasStringency with Serializable

   Converts internal rows with the provided schema into HTSJDK variant context.

7.  class LineIteratorImpl extends LineIterator with Iterator[String]
8.  case class ParsedFilterResult(contig: FilterContig, startInterval: FilterInterval, endInterval: FilterInterval) extends Product with Serializable
9.  sealed trait SampleIdInfo extends AnyRef
10.  case class SampleIds(unsortedSampleIds: Seq[String]) extends SampleIdInfo with Product with Serializable
11.  class VCFFileFormat extends TextBasedFileFormat with DataSourceRegister with HlsEventRecorder
12.  class VCFFileWriter extends OutputWriter with GlowLogging
13.  class VCFInputFormatter extends InputFormatter with GlowLogging

    An input formatter that writes rows as VCF records.

14.  class VCFInputFormatterFactory extends InputFormatterFactory
15.  class VCFOutputFormatter extends OutputFormatter with GlowLogging
16.  class VCFOutputFormatterFactory extends OutputFormatterFactory
17.  class VCFRowToVariantContextConverter extends Serializable

    VCFRow -> HTSJDK VariantContext Under the hood, this class relies on a InternalRowToVariantContextConverter.

18.  class VCFStreamWriter extends Closeable with Serializable

    This internal row -> variant context stream writer maintains a header that is set exactly once.

    This internal row -> variant context stream writer maintains a header that is set exactly once. The sample IDs are set by sampleIdInfo if predetermined, or inferred from the first written row otherwise.

    If missing sample IDs were used to set the header, sample IDs in all rows to be written will be replaced with those from the header. If all sample IDs are present when setting the header, sample IDs in written rows will not be replaced. Mixed missing/present sample IDs are not permitted.

19.  class VariantContextToInternalRowConverter extends GlowLogging with HasStringency with Serializable

    Converts an HTSJDK variant context into a SparkSQL row with the provided schema.

20.  class VariantContextToVCFRowConverter extends GlowLogging with Serializable
21.  case class VariantContextWrapper(vc: VariantContext, splitFromMultiallelic: Boolean) extends Product with Serializable