ADAMShell

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. val alignmentHeaders: Array[ASCIITableHeader]

   

   Alignment headers.

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. val featureHeaders: Array[ASCIITableHeader]

   

   Feature headers.

10. def finalize(): Unit

    

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11. val genotypeHeaders: Array[ASCIITableHeader]

    

    Genotype headers.

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

    

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13. def hashCode(): Int

    

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14. final def isInstanceOf[T0]: Boolean

    

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

    

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16. final def notify(): Unit

    

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17. final def notifyAll(): Unit

    

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18. def printAlignmentAttributes(alignments: Seq[Alignment], keys: Seq[String]): Unit

    

    Print attribute values for the specified alignments.

    Print attribute values for the specified alignments.

    alignments

    Sequence of alignments.

    keys

    Sequence of attribute keys.

19. def printAlignmentAttributes(alignments: AlignmentDataset, keys: Seq[String] = Seq.empty, limit: Int = 10): Unit

    

    Print attribute values for alignments in the specified AlignmentDataset up to the limit.

    Print attribute values for alignments in the specified AlignmentDataset up to the limit.

    alignments

    AlignmentDataset.

    keys

    Sequence of attribute keys. Defaults to empty.

    limit

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

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

    

    Print attribute values for the specified features.

    Print attribute values for the specified features.

    features

    Sequence of features.

    keys

    Sequence of attribute keys.

21. def printFeatureAttributes(features: FeatureDataset, keys: Seq[String] = Seq.empty, limit: Int = 10): Unit

    

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

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

    features

    FeatureDataset.

    keys

    Sequence of attribute keys. Defaults to empty.

    limit

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

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

    

    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.

23. def printFormatFields(genotypes: GenotypeDataset, keys: Seq[String] = Seq.empty, limit: Int = 10): Unit

    

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

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

    genotypes

    GenotypeDataset.

    keys

    Sequence of VCF FORMAT field attribute keys. Defaults to empty.

    limit

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

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

    

    Print genotype filter values for the specified genotypes.

    Print genotype filter values for the specified genotypes.

    genotypes

    Sequence of genotypes.

    headerLines

    Sequence of VCF header lines.

25. def printGenotypeFilters(genotypes: GenotypeDataset, limit: Int = 10): Unit

    

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

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

    genotypes

    GenotypeDataset.

    limit

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

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

    

    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. Defaults to empty.

    headerLines

    Sequence of VCF header lines.

27. def printInfoFields(variants: VariantDataset, keys: Seq[String] = Seq.empty, limit: Int = 10): Unit

    

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

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

    variants

    VariantDataset.

    keys

    Sequence of VCF INFO field attribute keys. Defaults to empty.

    limit

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

28. def printReadAttributes(reads: Seq[Read], keys: Seq[String]): Unit

    

    Print attribute values for the specified reads.

    Print attribute values for the specified reads.

    reads

    Sequence of reads.

    keys

    Sequence of attribute keys.

29. def printReadAttributes(reads: ReadDataset, keys: Seq[String] = Seq.empty, limit: Int = 10): Unit

    

    Print attribute values for reads in the specified ReadDataset up to the limit.

    Print attribute values for reads in the specified ReadDataset up to the limit.

    reads

    ReadDataset.

    keys

    Sequence of attribute keys. Defaults to empty.

    limit

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

30. def printSampleAttributes(samples: Seq[Sample], keys: Seq[String] = Seq.empty): Unit

    

    Print attribute values for the specified samples.

    Print attribute values for the specified samples.

    samples

    Sequence of samples.

    keys

    Sequence of attribute keys. Defaults to empty.

31. def printSequenceAttributes(sequences: Seq[Sequence], keys: Seq[String]): Unit

    

    Print attribute values for the specified sequences.

    Print attribute values for the specified sequences.

    sequences

    Sequence of sequences.

    keys

    Sequence of attribute keys.

32. def printSequenceAttributes(sequences: SequenceDataset, keys: Seq[String] = Seq.empty, limit: Int = 10): Unit

    

    Print attribute values for sequences in the specified SequenceDataset up to the limit.

    Print attribute values for sequences in the specified SequenceDataset up to the limit.

    sequences

    SequenceDataset.

    keys

    Sequence of attribute keys. Defaults to empty.

    limit

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

33. def printSliceAttributes(slices: Seq[Slice], keys: Seq[String]): Unit

    

    Print attribute values for the specified slices.

    Print attribute values for the specified slices.

    slices

    Sequence of slices.

    keys

    Sequence of attribute keys.

34. def printSliceAttributes(slices: SliceDataset, keys: Seq[String] = Seq.empty, limit: Int = 10): Unit

    

    Print attribute values for slices in the specified SliceDataset up to the limit.

    Print attribute values for slices in the specified SliceDataset up to the limit.

    slices

    SliceDataset.

    keys

    Sequence of attribute keys. Defaults to empty.

    limit

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

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

    

    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.

36. def printVariantFilters(variants: VariantDataset, limit: Int = 10): Unit

    

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

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

    variants

    VariantDataset.

    limit

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

37. val readHeaders: Array[ASCIITableHeader]

    

    Read headers.

38. val sequenceHeaders: Array[ASCIITableHeader]

    

    Sequence headers.

39. val sliceHeaders: Array[ASCIITableHeader]

    

    Slice headers.

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

    

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41. def toString(): String

    

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42. val variantHeaders: Array[ASCIITableHeader]

    

    Variant headers.

43. final def wait(): Unit

    

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

    

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

    

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