org.hammerlab.guacamole.reads

UnmappedRead

case class UnmappedRead(name: String, sequence: IndexedSeq[Byte], baseQualities: IndexedSeq[Byte], isDuplicate: Boolean, sampleId: SampleId, failedVendorQualityChecks: Boolean, isPaired: Boolean) extends Read with Product with Serializable

An unmapped read. See the Read trait for field descriptions.

Linear Supertypes
Serializable, Serializable, Product, Equals, Read, HasSampleId, AnyRef, Any
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Inherited
  1. UnmappedRead
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. Read
  7. HasSampleId
  8. AnyRef
  9. Any
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Instance Constructors

  1. new UnmappedRead(name: String, sequence: IndexedSeq[Byte], baseQualities: IndexedSeq[Byte], isDuplicate: Boolean, sampleId: SampleId, failedVendorQualityChecks: Boolean, isPaired: Boolean)

Value Members

  1. final def !=(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  2. final def !=(arg0: Any): Boolean

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

  4. final def ==(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  5. final def ==(arg0: Any): Boolean

    Definition Classes
    Any

  6. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  7. def asMappedRead: None.type

    Definition Classes
    UnmappedRead → Read

  8. val baseQualities: IndexedSeq[Byte]

    The base qualities, phred scaled.

    The base qualities, phred scaled. These are numbers, and are NOT character encoded.

    Definition Classes
    UnmappedRead → Read

  9. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  10. final def eq(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  11. val failedVendorQualityChecks: Boolean

    Whether the read failed predefined vendor checks for quality

    Whether the read failed predefined vendor checks for quality

    Definition Classes
    UnmappedRead → Read

  12. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

  13. final def getClass(): Class[_]

    Definition Classes
    AnyRef → Any

  14. val isDuplicate: Boolean

    Is this read a duplicate of another?

    Is this read a duplicate of another?

    Definition Classes
    UnmappedRead → Read

  15. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  16. val isMapped: Boolean

    Is this read mapped?

    Is this read mapped?

    Definition Classes
    UnmappedRead → Read

  17. val isPaired: Boolean

    Whether read is from a paired-end library

    Whether read is from a paired-end library

    Definition Classes
    UnmappedRead → Read

  18. val name: String

    Definition Classes
    UnmappedRead → Read

  19. final def ne(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  20. final def notify(): Unit

    Definition Classes
    AnyRef

  21. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  22. val sampleId: SampleId

    Definition Classes
    UnmappedRead → HasSampleId

  23. val sequence: IndexedSeq[Byte]

    The nucleotide sequence.

    The nucleotide sequence.

    Definition Classes
    UnmappedRead → Read

  24. final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
    AnyRef

  25. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  26. final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  27. final def wait(arg0: Long): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from Read

Inherited from HasSampleId

Inherited from AnyRef

Inherited from Any

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