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

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

models

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

rdd

GenomicDataset(jvmRdd, sc) Wraps an RDD of genomic data with helpful metadata.
VCFSupportingGenomicDataset(jvmRdd, sc) Wraps an GenomicDataset with VCF metadata.
AlignmentRecordRDD
CoverageRDD
FeatureRDD
FragmentRDD
GenotypeRDD
NucleotideContigFragmentRDD
VariantRDD
VariantContextRDD

stringency

STRICT htsjdk.samtools.ValidationStringency.STRICT
LENIENT htsjdk.samtools.ValidationStringency.LENIENT
SILENT htsjdk.samtools.ValidationStringency.SILENT