c

org.bdgenomics.adam.rdd.variant

VCFOutFormatter

case class VCFOutFormatter(conf: Configuration, stringency: ValidationStringency, optHeaderLines: Option[CollectionAccumulator[VCFHeaderLine]]) extends OutFormatter[VariantContext] with Logging with Product with Serializable

OutFormatter that reads streaming VCF.

conf

Hadoop configuration.

stringency

Validation stringency.

optHeaderLines

Optional accumulator for VCF header lines.

Linear Supertypes
Product, Equals, Logging, OutFormatter[VariantContext], Serializable, Serializable, AnyRef, Any
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Inherited
  1. VCFOutFormatter
  2. Product
  3. Equals
  4. Logging
  5. OutFormatter
  6. Serializable
  7. Serializable
  8. AnyRef
  9. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new VCFOutFormatter(conf: Configuration, optHeaderLines: Option[CollectionAccumulator[VCFHeaderLine]])

    OutFormatter that reads streaming VCF.

    OutFormatter that reads streaming VCF. Defaults to ValidationStringency.LENIENT. Java-friendly constructor.

    conf

    Hadoop configuration.

    optHeaderLines

    Optional accumulator for VCF header lines.

  2. new VCFOutFormatter(conf: Configuration, acc: CollectionAccumulator[VCFHeaderLine])

    OutFormatter that reads streaming VCF.

    OutFormatter that reads streaming VCF. Defaults to ValidationStringency.LENIENT. Java-friendly constructor.

    conf

    Hadoop configuration.

    acc

    Accumulator for VCF header lines.

  3. new VCFOutFormatter(conf: Configuration, stringency: ValidationStringency)

    OutFormatter that reads streaming VCF.

    OutFormatter that reads streaming VCF. Java-friendly constructor.

    conf

    Hadoop configuration.

  4. new VCFOutFormatter(conf: Configuration)

    OutFormatter that reads streaming VCF.

    OutFormatter that reads streaming VCF. Defaults to ValidationStringency.LENIENT. Java-friendly no-arg constructor.

    conf

    Hadoop configuration.

  5. new VCFOutFormatter(conf: Configuration, stringency: ValidationStringency, optHeaderLines: Option[CollectionAccumulator[VCFHeaderLine]])

    conf

    Hadoop configuration.

    stringency

    Validation stringency.

    optHeaderLines

    Optional accumulator for VCF header lines.

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  4. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  5. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  6. val conf: Configuration
  7. def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  8. def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  9. def debug(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  10. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  11. def error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  12. def error(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  13. def error(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  14. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  15. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  16. def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  17. def info(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  18. def info(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  19. def isDebugEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  20. def isErrorEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  21. def isInfoEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  22. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  23. def isTraceEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  24. def isWarnEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  25. def logger: Logger
    Attributes
    protected
    Definition Classes
    Logging
  26. def loggerName: String
    Attributes
    protected
    Definition Classes
    Logging
  27. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  28. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  29. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  30. val optHeaderLines: Option[CollectionAccumulator[VCFHeaderLine]]
  31. def read(is: InputStream): Iterator[VariantContext]

    Reads VariantContexts from an input stream.

    Reads VariantContexts from an input stream. Autodetects VCF format.

    is

    An InputStream connected to a process we are piping from.

    returns

    Returns an iterator of Alignments read from the stream.

    Definition Classes
    VCFOutFormatter → OutFormatter
  32. val stringency: ValidationStringency
  33. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  34. def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  35. def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  36. def trace(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  37. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  38. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
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    @throws( ... )
  39. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  40. def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  41. def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  42. def warn(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging

Inherited from Product

Inherited from Equals

Inherited from Logging

Inherited from OutFormatter[VariantContext]

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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