object ADAMShell
Utility methods for use in adam-shell.
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val
alignmentHeaders: Array[ASCIITableHeader]
Alignment record headers.
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def
createMetricsListener(sc: SparkContext): MetricsListener
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.
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eq(arg0: AnyRef): Boolean
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equals(arg0: Any): Boolean
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val
featureHeaders: Array[ASCIITableHeader]
Feature headers.
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finalize(): Unit
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val
genotypeHeaders: Array[ASCIITableHeader]
Genotype headers.
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notify(): Unit
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notifyAll(): Unit
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def
printAlignmentAttributes(alignments: Seq[AlignmentRecord], keys: Seq[String]): Unit
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.
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def
printAlignmentAttributes(alignments: AlignmentRecordDataset, keys: Seq[String], limit: Int = 10): Unit
Print attribute values for alignment records in the specified AlignmentRecordDataset up to the limit.
Print attribute values for alignment records in the specified AlignmentRecordDataset up to the limit.
- alignments
AlignmentRecordDataset.
- keys
Sequence of attribute keys.
- limit
Number of alignment records 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.
- keys
Sequence of attribute keys.
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def
printFeatureAttributes(features: FeatureDataset, keys: Seq[String], 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.
- 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], 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.
- 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.
- headerLines
Sequence of VCF header lines.
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def
printInfoFields(variants: VariantDataset, keys: Seq[String], 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.
- limit
Number of variants to print VCF INFO field attribute values for. Defaults to 10.
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def
printMetrics(totalTime: Long, metricsListener: MetricsListener): Unit
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.
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def
printMetrics(metricsListener: MetricsListener): Unit
Print metrics gathered by the specified metrics listener.
Print metrics gathered by the specified metrics listener.
- metricsListener
Metrics listener.
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def
printSampleAttributes(samples: Seq[Sample], keys: Seq[String]): Unit
Print attribute values for the specified samples.
Print attribute values for the specified samples.
- samples
Sequence of samples.
- keys
Sequence of attribute keys.
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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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synchronized[T0](arg0: ⇒ T0): T0
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def
toString(): String
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val
variantHeaders: Array[ASCIITableHeader]
Variant headers.
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wait(): Unit
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wait(arg0: Long, arg1: Int): Unit
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