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 GenomicDatset with VCF metadata.
AlignmentRecordRDD(jvmRdd, sc) Wraps an GenomicDatset with Alignment Record metadata and functions.
CoverageRDD(jvmRdd, sc) Wraps an GenomicDatset with Coverage metadata and functions.
FeatureRDD(jvmRdd, sc) Wraps an GenomicDatset with Feature metadata and functions.
FragmentRDD(jvmRdd, sc) Wraps an GenomicDatset with Fragment metadata and functions.
GenotypeRDD(jvmRdd, sc) Wraps an GenomicDatset with Genotype metadata and functions.
NucleotideContigFragmentRDD(jvmRdd, sc) Wraps an GenomicDatset with Nucleotide Contig Fragment metadata and functions.
VariantRDD(jvmRdd, sc) Wraps an GenomicDatset with Variant metadata and functions.
VariantContextRDD(jvmRdd, sc) Wraps an GenomicDataset with Variant Context metadata and functions.

stringency

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