Object

org.bdgenomics.adam.util

ADAMShell

Related Doc: package util

Permalink

object ADAMShell

Utility methods for use in adam-shell.

Linear Supertypes
AnyRef, Any
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. ADAMShell
  2. AnyRef
  3. Any
  1. Hide All
  2. Show All
Visibility
  1. Public
  2. All

Value Members

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

    Permalink
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int

    Permalink
    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean

    Permalink
    Definition Classes
    AnyRef → Any
  4. val alignmentHeaders: Array[ASCIITableHeader]

    Permalink

    Alignment record headers.

  5. final def asInstanceOf[T0]: T0

    Permalink
    Definition Classes
    Any
  6. def clone(): AnyRef

    Permalink
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  7. def createMetricsListener(sc: SparkContext): MetricsListener

    Permalink

    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.

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

    Permalink
    Definition Classes
    AnyRef
  9. def equals(arg0: Any): Boolean

    Permalink
    Definition Classes
    AnyRef → Any
  10. val featureHeaders: Array[ASCIITableHeader]

    Permalink

    Feature headers.

  11. def finalize(): Unit

    Permalink
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  12. val genotypeHeaders: Array[ASCIITableHeader]

    Permalink

    Genotype headers.

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

    Permalink
    Definition Classes
    AnyRef → Any
  14. def hashCode(): Int

    Permalink
    Definition Classes
    AnyRef → Any
  15. final def isInstanceOf[T0]: Boolean

    Permalink
    Definition Classes
    Any
  16. final def ne(arg0: AnyRef): Boolean

    Permalink
    Definition Classes
    AnyRef
  17. final def notify(): Unit

    Permalink
    Definition Classes
    AnyRef
  18. final def notifyAll(): Unit

    Permalink
    Definition Classes
    AnyRef
  19. def printAlignmentAttributes(alignments: Seq[AlignmentRecord], keys: Seq[String]): Unit

    Permalink

    Print attribute values for the specified alignment records.

    Print attribute values for the specified alignment records.

    alignments

    Sequence of alignments.

    keys

    Sequence of attribute keys.

  20. def printAlignmentAttributes(rdd: AlignmentRecordRDD, keys: Seq[String], limit: Int = 10): Unit

    Permalink

    Print attribute values for alignment records in the specified rdd up to the limit.

    Print attribute values for alignment records in the specified rdd up to the limit.

    rdd

    AlignmentRecordRDD.

    keys

    Sequence of attribute keys.

    limit

    Number of alignment records to print attribute values for. Defaults to 10.

  21. def printFeatureAttributes(features: Seq[Feature], keys: Seq[String]): Unit

    Permalink

    Print attribute values for the specified features.

    Print attribute values for the specified features.

    keys

    Sequence of attribute keys.

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

    Permalink

    Print attribute values for features in the specified rdd up to the limit.

    Print attribute values for features in the specified rdd up to the limit.

    rdd

    FeatureRDD.

    keys

    Sequence of attribute keys.

    limit

    Number of features to print attribute values for. Defaults to 10.

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

    Permalink

    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.

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

    Permalink

    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.

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

    Permalink

    Print genotype filter values for the specified genotypes.

    Print genotype filter values for the specified genotypes.

    headerLines

    Sequence of VCF header lines.

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

    Permalink

    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.

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

    Permalink

    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.

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

    Permalink

    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.

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

    Permalink

    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.

  30. def printMetrics(metricsListener: MetricsListener): Unit

    Permalink

    Print metrics gathered by the specified metrics listener.

    Print metrics gathered by the specified metrics listener.

    metricsListener

    Metrics listener.

  31. def printSampleAttributes(samples: Seq[Sample], keys: Seq[String]): Unit

    Permalink

    Print attribute values for the specified features.

    Print attribute values for the specified features.

    keys

    Sequence of attribute keys.

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

    Permalink

    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.

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

    Permalink

    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.

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

    Permalink
    Definition Classes
    AnyRef
  35. def toString(): String

    Permalink
    Definition Classes
    AnyRef → Any
  36. val variantHeaders: Array[ASCIITableHeader]

    Permalink

    Variant headers.

  37. final def wait(): Unit

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  38. final def wait(arg0: Long, arg1: Int): Unit

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  39. final def wait(arg0: Long): Unit

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from AnyRef

Inherited from Any

Ungrouped