Object/Trait

org.hammerlab.genomics.reads

Read

Related Docs: trait Read | package reads

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object Read extends Logging

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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. def apply(alignmentRecord: AlignmentRecord, sampleId: Int)(implicit cf: Factory): Read

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    Builds a Guacamole Read from and ADAM Alignment Record

    Builds a Guacamole Read from and ADAM Alignment Record

    alignmentRecord

    ADAM Alignment Record (an aligned or unaligned read)

    returns

    Mapped or Unmapped Read

  5. def apply(record: SAMRecord)(implicit cf: Factory): Read

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    Convert a SAM tools record into a Read.

  6. final def asInstanceOf[T0]: T0

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  7. def baseQualityStringToArray(baseQualities: String, length: Int): Array[Byte]

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    Converts the ascii-string encoded base qualities into an array of integers quality scores in Phred-scale

    Converts the ascii-string encoded base qualities into an array of integers quality scores in Phred-scale

    baseQualities

    Base qualities of a read (ascii-encoded)

    length

    Length of the read sequence

    returns

    Base qualities in Phred scale

  8. def clone(): AnyRef

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  9. def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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  10. def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit

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  11. def debug(msg: ⇒ Any): Unit

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

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  13. def equals(arg0: Any): Boolean

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  14. def error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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  15. def error(msg: ⇒ Any, t: ⇒ Throwable): Unit

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  16. def error(msg: ⇒ Any): Unit

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  17. def finalize(): Unit

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

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  19. def hashCode(): Int

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  20. def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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  21. def info(msg: ⇒ Any, t: ⇒ Throwable): Unit

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  22. def info(msg: ⇒ Any): Unit

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  23. def isDebugEnabled: Boolean

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  24. def isErrorEnabled: Boolean

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  25. def isInfoEnabled: Boolean

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  26. final def isInstanceOf[T0]: Boolean

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  27. def isTraceEnabled: Boolean

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  28. def isWarnEnabled: Boolean

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  29. def logger: Logger

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  30. def loggerName: String

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

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  32. final def notify(): Unit

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  33. final def notifyAll(): Unit

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

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  35. def toString(): String

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  36. def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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  37. def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit

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  38. def trace(msg: ⇒ Any): Unit

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  39. final def wait(): Unit

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

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

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  42. def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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  43. def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit

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  44. def warn(msg: ⇒ Any): Unit

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