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

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

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3. final def ##(): Int

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4. final def ==(arg0: AnyRef): Boolean

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5. final def ==(arg0: Any): Boolean

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6. def apply(alignmentRecord: AlignmentRecord, sampleId: Int): Read

   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

7. def apply(record: SAMRecord, sampleId: Int): Read

   Convert a SAM tools record into a Read.

   Convert a SAM tools record into a Read.

   record

   returns

8. final def asInstanceOf[T0]: T0

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

   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

10. def clone(): AnyRef

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

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12. def debug(msg: ⇒ Any): Unit

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

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14. def equals(arg0: Any): Boolean

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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(msg: ⇒ Any, t: ⇒ Throwable): Unit

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21. def info(msg: ⇒ Any): Unit

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22. def isDebugEnabled: Boolean

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23. def isErrorEnabled: Boolean

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24. def isInfoEnabled: Boolean

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25. final def isInstanceOf[T0]: Boolean

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26. def isTraceEnabled: Boolean

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27. def isWarnEnabled: Boolean

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28. def logger: Logger

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29. def loggerName: String

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

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31. final def notify(): Unit

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32. final def notifyAll(): Unit

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

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34. def toString(): String

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

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36. def trace(msg: ⇒ Any): Unit

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37. final def wait(): Unit

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

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

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

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41. def warn(msg: ⇒ Any): Unit

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