object ADAMShell
Utility methods for use in adam-shell.
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val
alignmentHeaders: Array[ASCIITableHeader]
Alignment headers.
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val
featureHeaders: Array[ASCIITableHeader]
Feature headers.
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val
genotypeHeaders: Array[ASCIITableHeader]
Genotype headers.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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val
readHeaders: Array[ASCIITableHeader]
Read headers.
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val
sequenceHeaders: Array[ASCIITableHeader]
Sequence headers.
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val
sliceHeaders: Array[ASCIITableHeader]
Slice headers.
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def
toString(): String
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val
variantHeaders: Array[ASCIITableHeader]
Variant headers.
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