object UmiConsensusCaller

Contains shared types and functions used when writing UMI-driven consensus callers that take in SAMRecords and emit SAMRecords.

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Type Members

  1. trait SimpleRead extends AnyRef

    A trait that consensus reads must implement.

  2. case class SourceRead (id: String, bases: Array[Byte], quals: Array[Byte]) extends SimpleRead with Product with Serializable

    Stores information about a read to be fed into a consensus.

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  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. final def asInstanceOf[T0]: T0
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  5. def clone(): AnyRef
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  6. final def eq(arg0: AnyRef): Boolean
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  8. def finalize(): Unit
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  9. final def getClass(): Class[_]
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  10. def hashCode(): Int
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  11. final def isInstanceOf[T0]: Boolean
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  12. def makePrefixFromSamHeader(header: SAMFileHeader): String

    Attempts to construct a String that can be used as a prefix for consensus read names based on the contents of the incoming SAMFileHeader.

  13. final def ne(arg0: AnyRef): Boolean
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  14. final def notify(): Unit
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  15. final def notifyAll(): Unit
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  16. def outputHeader(in: SAMFileHeader, readGroupId: String, sortOrder: Option[SortOrder] = None): SAMFileHeader

    Constructs an output header with a single read group for the a BAM.

  17. final def synchronized[T0](arg0: ⇒ T0): T0
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  18. def toString(): String
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  19. final def wait(): Unit
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  20. final def wait(arg0: Long, arg1: Int): Unit
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  21. final def wait(arg0: Long): Unit
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  22. object ReadType extends Enumeration

    The type of consensus read to output.

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