TrioCaller

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(rdd: GenotypeRDD, firstParentId: String, secondParentId: String, childId: String): GenotypeRDD

   

   Trio calls genotypes in a pedigree with two parents and one child.

   Trio calls genotypes in a pedigree with two parents and one child.

   rdd

   RDD of base genotypes.

   firstParentId

   The sample ID for the first parent.

   secondParentId

   The sample ID for the second parent.

   childId

   The sample ID for the child.

   returns

   Returns the final genotypes.

5. final def asInstanceOf[T0]: T0

   

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6. def clone(): AnyRef

   

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

   

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8. def equals(arg0: Any): Boolean

   

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9. def extractSampleId(rdd: AlignmentRecordRDD): String

   

   Extracts the sample ID from a set of reads.

   Extracts the sample ID from a set of reads.

   Requires that read groups are attached, and that all read groups are from a single sample.

   rdd

   The reads to extract the sample ID from.

   returns

   The sample ID.

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. 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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