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org.bdgenomics.adam.util

ADAMShell

Related Doc: package util

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object ADAMShell

Utility methods for use in adam-shell.

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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. def createMetricsListener(sc: SparkContext): MetricsListener

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    Create and return a new metrics listener for the specified Spark context.

    Create and return a new metrics listener for the specified Spark context.

    sc

    Spark context.

    returns

    Return a new metrics listener for the specified Spark context.

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

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  8. def equals(arg0: Any): Boolean

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  9. def finalize(): Unit

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  10. val genotypeHeaders: Array[ASCIITableHeader]

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    Genotype headers.

  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. def printFormatFields(genotypes: Seq[Genotype], keys: Seq[String], headerLines: Seq[VCFHeaderLine]): Unit

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    Print VCF FORMAT field attributes for the specified genotypes.

    Print VCF FORMAT field attributes for the specified genotypes.

    genotypes

    Sequence of genotypes.

    keys

    Sequence of VCF FORMAT field attribute keys.

    headerLines

    Sequence of VCF header lines.

  18. def printFormatFields(rdd: GenotypeRDD, keys: Seq[String], limit: Int = 10): Unit

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    Print VCF FORMAT field attributes for genotypes in the specified rdd up to the limit.

    Print VCF FORMAT field attributes for genotypes in the specified rdd up to the limit.

    rdd

    GenotypeRDD.

    keys

    Sequence of VCF FORMAT field attribute keys.

    limit

    Number of genotypes to print VCF FORMAT field attribute values for. Defaults to 10.

  19. def printGenotypeFilters(genotypes: Seq[Genotype], headerLines: Seq[VCFHeaderLine]): Unit

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    Print genotype filter values for the specified genotypes.

    Print genotype filter values for the specified genotypes.

    headerLines

    Sequence of VCF header lines.

  20. def printGenotypeFilters(rdd: GenotypeRDD, limit: Int = 10): Unit

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    Print genotype filter values for genotypes in the specified rdd up to the limit.

    Print genotype filter values for genotypes in the specified rdd up to the limit.

    rdd

    GenotypeRDD.

    limit

    Number of genotypes to print genotype filter values for. Defaults to 10.

  21. def printInfoFields(variants: Seq[Variant], keys: Seq[String], headerLines: Seq[VCFHeaderLine]): Unit

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    Print VCF INFO field attributes for the specified variants.

    Print VCF INFO field attributes for the specified variants.

    variants

    Sequence of variants.

    keys

    Sequence of VCF INFO field attribute keys.

    headerLines

    Sequence of VCF header lines.

  22. def printInfoFields(rdd: VariantRDD, keys: Seq[String], limit: Int = 10): Unit

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    Print VCF INFO field attributes for variants in the specified rdd up to the limit.

    Print VCF INFO field attributes for variants in the specified rdd up to the limit.

    rdd

    VariantRDD.

    keys

    Sequence of VCF INFO field attribute keys.

    limit

    Number of variants to print VCF INFO field attribute values for. Defaults to 10.

  23. def printMetrics(totalTime: Long, metricsListener: MetricsListener): Unit

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    Print metrics gathered by the specified metrics listener.

    Print metrics gathered by the specified metrics listener.

    totalTime

    Total execution time, in ns.

    metricsListener

    Metrics listener.

  24. def printMetrics(metricsListener: MetricsListener): Unit

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    Print metrics gathered by the specified metrics listener.

    Print metrics gathered by the specified metrics listener.

    metricsListener

    Metrics listener.

  25. def printVariantFilters(variants: Seq[Variant], headerLines: Seq[VCFHeaderLine]): Unit

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    Print filter values for the specified variants.

    Print filter values for the specified variants.

    variants

    Sequence of variants to print filter values for.

    headerLines

    Sequence of VCF header lines.

  26. def printVariantFilters(rdd: VariantRDD, limit: Int = 10): Unit

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    Print filter values for variants in the specified rdd up to the limit.

    Print filter values for variants in the specified rdd up to the limit.

    rdd

    VariantRDD.

    limit

    Number of variants to print filter values for. Defaults to 10.

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

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  28. def toString(): String

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  29. val variantHeaders: Array[ASCIITableHeader]

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    Variant headers.

  30. final def wait(): Unit

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

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

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