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object SamOrder

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Type Members

  1. case class CoordinateKey(refIndex: Int, pos: Int, flags: Int) extends Ordered[CoordinateKey] with Product with Serializable

    Ordered key object for Coordinate order.

  2. case class QuerynameKey(name: String, flags: Int) extends Ordered[QuerynameKey] with Product with Serializable

    Ordered key object for Queryname order.

  3. final case class RandomKey(hash: Int, flags: Int) extends Ordered[RandomKey] with Product with Serializable

    Key object used by Random and RandomQuery sorts.

  4. case class TemplateCoordinateKey(refIndex1: Int, refIndex2: Int, pos1: Int, pos2: Int, neg1: Boolean, neg2: Boolean, library: String, mid: String, name: String, isUpperOfPair: Boolean) extends Ordered[TemplateCoordinateKey] with Product with Serializable

    Sorting key used by the TemplateCoordinate sort.

Value Members

  1. final def !=(arg0: Any): Boolean
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  2. final def ##(): Int
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  3. final def ==(arg0: Any): Boolean
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  4. def apply(header: SAMFileHeader): Option[SamOrder]

    If the header represents a known sort order returns that SortOrder otherwise None.

  5. def apply(name: String): SamOrder

    Returns the SamOrder for the given name.

    Returns the SamOrder for the given name. Throws an exception if the name doesn't match a known ordering. Performs case insensitive matching so that we can use capitalized class names, but have backwards compatibility to SAM spec sort orders that are all lower-case.

  6. final def asInstanceOf[T0]: T0
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  7. def clone(): AnyRef
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  8. final def eq(arg0: AnyRef): Boolean
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  9. def equals(arg0: Any): Boolean
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  10. def finalize(): Unit
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  11. final def getClass(): Class[_]
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  12. def hashCode(): Int
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  13. final def isInstanceOf[T0]: Boolean
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  14. final def ne(arg0: AnyRef): Boolean
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  15. final def notify(): Unit
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  16. final def notifyAll(): Unit
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  17. final def synchronized[T0](arg0: ⇒ T0): T0
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  18. def toString(): String
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  19. val values: Seq[SamOrder]

    The set of all possible values.

  20. final def wait(): Unit
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  21. final def wait(arg0: Long, arg1: Int): Unit
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  22. final def wait(arg0: Long): Unit
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  23. object Coordinate extends SamOrder with Product with Serializable

    Ordering object for coordinate order per the SAM spec - reads without refIndex/coordinate are sorted to the end.

  24. object Queryname extends SamOrder with Product with Serializable

    Ordering object for queryname order per the SAM spec.

  25. object Random extends SamOrder with Product with Serializable

    Ordering object for generating a random order over all reads.

  26. object RandomQuery extends SamOrder with Product with Serializable

    Ordering object for generating a random order with queryname grouping.

  27. object TemplateCoordinate extends SamOrder with Product with Serializable

    The sort order used by GroupReadByUmi.

    The sort order used by GroupReadByUmi. Sorts reads by the earlier unclipped 5' coordinate of the read pair, the higher unclipped 5' coordinate of the read pair, library, the molecular identifier (see com.fulcrumgenomics.umi.ConsensusTags.MolecularId), read name, and if R1 has the lower coordinates of the pair.

  28. object Unknown extends SamOrder with Product with Serializable

    Ordering for the official "unknown" ordering.

  29. object Unsorted extends SamOrder with Product with Serializable

    Ordering for the official "unsorted" ordering.

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