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 alignments into an AlignmentDataset.
`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.