ADAM Python Documentation¶

bdgenomics.adam Package¶

ADAM’s Python API wraps the ADAMContext and GenomicDataset 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.

ds¶

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

stringency¶

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