c

io.projectglow.vcf

VCFStreamWriter

class VCFStreamWriter extends Closeable with Serializable

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.

Linear Supertypes
Serializable, Serializable, Closeable, AutoCloseable, AnyRef, Any
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Inherited
  1. VCFStreamWriter
  2. Serializable
  3. Serializable
  4. Closeable
  5. AutoCloseable
  6. AnyRef
  7. Any
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Visibility
  1. Public
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Instance Constructors

  1. new VCFStreamWriter(stream: OutputStream, headerLineSet: Set[VCFHeaderLine], sampleIdInfo: SampleIdInfo, writeHeader: Boolean)

    stream

    The stream to write to

    headerLineSet

    Header lines used to set the VCF header

    sampleIdInfo

    Sample IDs, which may be predetermined or must be inferred

    writeHeader

    Whether to write the header in this stream

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 checkInferredSampleIds(vcBuilder: VariantContextBuilder): VariantContextBuilder
  6. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  7. def close(): Unit
    Definition Classes
    VCFStreamWriter → Closeable → AutoCloseable
  8. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  9. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  10. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  11. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  12. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  13. var header: VCFHeader
  14. var headerSampleSet: HashSet[String]
  15. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  16. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  17. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  18. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  19. def replaceMissingSampleIds(vcBuilder: VariantContextBuilder): VariantContextBuilder
  20. var replaceSampleIds: Boolean
  21. def setHeader(vcBuilder: VariantContextBuilder): Unit
  22. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  23. def toString(): String
    Definition Classes
    AnyRef → Any
  24. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  25. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
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    @throws( ... )
  26. final def wait(arg0: Long): Unit
    Definition Classes
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    @native() @throws( ... )
  27. def write(vc: VariantContext): Unit

Inherited from Serializable

Inherited from Serializable

Inherited from Closeable

Inherited from AutoCloseable

Inherited from AnyRef

Inherited from Any

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