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], cigar: Cigar, sam: Option[SamRecord] = None) extends SimpleRead with Product with Serializable

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

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. val FilterInsufficientSupport: String

    Filter reason for when there are too few reads to form a consensus.

  5. val FilterLowQuality: String

    Filter reason for when reads are rejected due to low quality.

  6. val FilterMinorityAlignment: String

    Filter reason for when reads are rejected for having a minority CIGAR.

  7. val FilterOrphan: String

    Filter reason for when reads are rejected due creation of orphaned consensus (i.e.

    Filter reason for when reads are rejected due creation of orphaned consensus (i.e. R1 or R2 failed).

  8. final def asInstanceOf[T0]: T0
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  9. def clone(): AnyRef
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  10. final def eq(arg0: AnyRef): Boolean
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  11. def equals(arg0: Any): Boolean
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  12. def finalize(): Unit
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  13. final def getClass(): Class[_]
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  14. def hashCode(): Int
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  15. final def isInstanceOf[T0]: Boolean
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  16. 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.

  17. final def ne(arg0: AnyRef): Boolean
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  18. final def notify(): Unit
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  19. final def notifyAll(): Unit
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  20. def outputHeader(in: SAMFileHeader, readGroupId: String, sortOrder: Option[SamOrder] = None): SAMFileHeader

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

  21. final def synchronized[T0](arg0: ⇒ T0): T0
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  22. def toString(): String
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  23. final def wait(): Unit
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  24. final def wait(arg0: Long, arg1: Int): Unit
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  25. final def wait(arg0: Long): Unit
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  26. object ReadType extends Enumeration

    The type of consensus read to output.

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