ADAM Python Documentation

bdgenomics.adam Package

ADAM’s Python API wraps the ADAMContext and GenomicRDD APIs so they can be used from PySpark. The Python API is feature complete relative to ADAM’s Java API.


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


ReferenceRegion(referenceName, start, end) Represents a contiguous region of the reference genome.


GenomicDataset(jvmRdd, sc) Wraps an RDD of genomic data with helpful metadata.
VCFSupportingGenomicDataset(jvmRdd, sc) Wraps an GenomicDataset with VCF metadata.
AlignmentDataset(jvmRdd, sc) Wraps an GenomicDataset with alignment metadata and functions.
CoverageDataset(jvmRdd, sc) Wraps an GenomicDataset with Coverage metadata and functions.
FeatureDataset(jvmRdd, sc) Wraps an GenomicDataset with Feature metadata and functions.
FragmentDataset(jvmRdd, sc) Wraps an GenomicDataset with Fragment metadata and functions.
GenotypeDataset(jvmRdd, sc) Wraps an GenomicDataset with Genotype metadata and functions.
SequenceDataset(jvmRdd, sc)
SliceDataset(jvmRdd, sc)
VariantDataset(jvmRdd, sc) Wraps an GenomicDataset with Variant metadata and functions.
VariantContextDataset(jvmRdd, sc) Wraps an GenomicDataset with Variant Context metadata and functions.


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