Trait/Object

org.hammerlab.genomics.reads

Read

Related Docs: object Read | package reads

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trait Read extends AnyRef

The fields in the Read trait are common to any read, whether mapped (aligned) or not.

Linear Supertypes
AnyRef, Any
Known Subclasses
MappedRead, PairedRead, UnmappedRead
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Abstract Value Members

  1. abstract def asMappedRead: Option[MappedRead]

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  2. abstract def baseQualities: IndexedSeq[Byte]

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    The base qualities, phred scaled.

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

  3. abstract def failedVendorQualityChecks: Boolean

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    Whether the read failed predefined vendor checks for quality

  4. abstract def isDuplicate: Boolean

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    Is this read a duplicate of another?

  5. abstract def isMapped: Boolean

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    Is this read mapped?

  6. abstract def isPaired: Boolean

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    Whether read is from a paired-end library

  7. abstract def name: String

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  8. abstract def sequence: Bases

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    The nucleotide sequence.

Concrete Value Members

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

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    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

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    Definition Classes
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  3. final def ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  4. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  5. def clone(): AnyRef

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

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

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    Definition Classes
    AnyRef

  7. def equals(arg0: Any): Boolean

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    Definition Classes
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  8. def finalize(): Unit

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

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

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    Definition Classes
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  10. def hashCode(): Int

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    Definition Classes
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  11. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

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

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    Definition Classes
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  13. final def notify(): Unit

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    Definition Classes
    AnyRef

  14. final def notifyAll(): Unit

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    Definition Classes
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  15. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
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  16. def toString(): String

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    Definition Classes
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  17. final def wait(): Unit

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    Definition Classes
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    Annotations
    @throws( ... )

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

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    Definition Classes
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    Annotations
    @throws( ... )

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

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    Definition Classes
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    @throws( ... )

Inherited from AnyRef

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