bdgenomics.adam.adamContext.ADAMContext

class bdgenomics.adam.adamContext.ADAMContext(ss)[source]

The ADAMContext provides functions on top of a SparkContext for loading genomic data.

__init__(ss)[source]

Initializes an ADAMContext using a SparkSession.

Parameters:ss – The currently active pyspark.context.SparkContext.

Methods

__init__(ss) Initializes an ADAMContext using a SparkSession.
loadAlignments(filePath[, stringency]) Load alignment records into an AlignmentRecordDataset.
loadCoverage(filePath[, stringency]) Load features into a FeatureDataset and convert to a CoverageDataset.
loadDnaSequences(filePath) Load DNA sequences into a SequenceDataset.
loadFeatures(filePath[, stringency]) Load features into a FeatureDataset.
loadFragments(filePath[, stringency]) Load fragments into a FragmentDataset.
loadGenotypes(filePath[, stringency]) Load genotypes into a GenotypeDataset.
loadIndexedBam(filePath, viewRegions[, …]) Functions like loadAlignments, but uses BAM index files to look at fewer blocks, and only returns records within the specified ReferenceRegions.
loadProteinSequences(filePath) Load protein sequences into a SequenceDataset.
loadRnaSequences(filePath) Load RNA sequences into a SequenceDataset.
loadSlices(filePath, maximumLength) Load slices into a SliceDataset.
loadVariants(filePath[, stringency]) Load variants into a VariantDataset.