Working with genomic data using GenomicRDDs

As described in the section on using the ADAMContext, ADAM loads genomic data into a GenomicRDD which is specialized for each datatype. This GenomicRDD wraps Apache Spark’s Resilient Distributed Dataset (RDD, (Zaharia et al. 2012)) API with genomic metadata. The RDD abstraction presents an array of data which is distributed across a cluster. RDDs are backed by a computational lineage, which allows them to be recomputed if a node fails and the results of a computation are lost. RDDs are processed by running functional transformations across the whole dataset.

Around an RDD, ADAM adds metadata which describes the genome, samples, or read group that a dataset came from. Specifically, ADAM supports the following metadata:

  • GenomicRDD base: A sequence dictionary, which describes the reference assembly that data are aligned to, if it is aligned. Applies to all types.
  • MultisampleGenomicRDD: Adds metadata about the samples in a dataset. Applies to GenotypeRDD.
  • ReadGroupGenomicRDD: Adds metadata about the read groups attached to a dataset. Applies to AlignmentRecordRDD and FragmentRDD.

Additionally, GenotypeRDD, VariantRDD, and VariantContextRDD store the VCF header lines attached to the original file, to enable a round trip between Parquet and VCF.

GenomicRDDs can be transformed several ways. These include:

Transforming GenomicRDDs

Although GenomicRDDs do not extend Apache Spark’s RDD class, RDD operations can be performed on them using the transform method. Currently, we only support RDD to RDD transformations that keep the same type as the base type of the GenomicRDD. To apply an RDD transform, use the transform method, which takes a function mapping one RDD of the base type into another RDD of the base type. For example, we could use transform on an AlignmentRecordRDD to filter out reads that have a low mapping quality, but we cannot use transform to translate those reads into Features showing the genomic locations covered by reads.

If we want to transform a GenomicRDD into a new GenomicRDD that contains a different datatype (e.g., reads to features), we can instead use the transmute function. The transmute function takes a function that transforms an RDD of the type of the first GenomicRDD into a new RDD that contains records of the type of the second GenomicRDD. Additionally, it takes an implicit function that maps the metadata in the first GenomicRDD into the metadata needed by the second GenomicRDD. This is akin to the implicit function required by the pipe API. As an example, let us use the transmute function to make features corresponding to reads containing INDELs:

// pick up implicits from ADAMContext
import org.bdgenomics.adam.rdd.ADAMContext._

val reads = sc.loadAlignments("path/to/my/reads.adam")

// the type of the transmuted RDD normally needs to be specified
// import the FeatureRDD, which is the output type
import org.bdgenomics.adam.rdd.feature.FeatureRDD
import org.bdgenomics.formats.avro.Feature

val features: FeatureRDD = reads.transmute(rdd => {
  rdd.filter(r => {
    // does the CIGAR for this read contain an I or a D?
    Option(r.getCigar)
      .exists(c => c.contains("I") || c.contains("D"))
  }).map(r => {
    Feature.newBuilder
      .setContigName(r.getContigName)
      .setStart(r.getStart)
      .setEnd(r.getEnd)
      .build
  })
})

ADAMContext provides the implicit functions needed to run the transmute function between all GenomicRDDs contained within the org.bdgenomics.adam.rdd package hierarchy. Any custom GenomicRDD can be supported by providing a user defined conversion function.

Transforming GenomicRDDs via Spark SQL

Spark SQL introduced the strongly-typed Dataset API in Spark 1.6.0. This API supports seamless translation between the RDD API and a strongly typed DataFrame style API. While Spark SQL supports many types of encoders for translating data from an RDD into a Dataset, no encoders support the Avro models used by ADAM to describe our genomic schemas. In spite of this, Spark SQL is highly desirable because it has a more efficient execution engine than the Spark RDD APIs, which can lead to substantial speedups for certain queries.

To resolve this, we added an adam-codegen package that generates Spark SQL compatible classes representing the ADAM schemas. These classes are available in the org.bdgenomics.adam.sql package. All Avro-backed GenomicRDDs now support translation to Datasets via the dataset field, and transformation via the Spark SQL APIs through the transformDataset method. As an optimization, we lazily choose either the RDD or Dataset API depending on the calculation being performed. For example, if one were to load a Parquet file of reads, we would not decide to load the Parquet file as an RDD or a Dataset until we saw your query. If you were to load the reads from Parquet and then were to immediately run a transformDataset call, it would be more efficient to load the data directly using the Spark SQL APIs, instead of loading the data as an RDD, and then transforming that RDD into a SQL Dataset.

The functionality of the adam-codegen package is simple. The goal of this package is to take ADAM’s Avro schemas and to remap them into classes that implement Scala’s Product interface, and which have a specific style of constructor that is expected by Spark SQL. Additionally, we define functions that translate between these Product classes and the bdg-formats Avro models. Parquet files written with either the Product classes and Spark SQL Parquet writer or the Avro classes and the RDD/ParquetAvroOutputFormat are equivalent and can be read through either API. However, to support this, we must explicitly set the requested schema on read when loading data through the RDD read path. This is because Spark SQL writes a Parquet schema that is equivalent but not strictly identical to the Parquet schema that the Avro/RDD write path writes. If the schema is not set, then schema validation on read fails. If reading data using the ADAMContext APIs, this is handled properly; this is an implementation note necessary only for those bypassing the ADAM APIs.

Similar to transform/transformDataset, there exists a transmuteDataset function that enables transformations between GenomicRDDs of different types.

Using partitioned Parquet to speed up range based queries

GenomicRDDs of types AlignmentRecordRDD, GenotypeRDD, VariantRDD, and NucleotideFragmentContigRDD can be written as Parquet using a Hive-style hierarchical directory scheme that is based on contig and genomic position. This partitioning reduces the latency of genomic range queries against these datasets, which is particularly important for interactive applications such as a genomic browser backed by an ADAM dataset.

The genomicRDD function GenomicRDD.filterByOverlappingRegions(queryRegionsList) builds a Spark SQL query that uses this partitioning scheme. This can reduce latencies by more than 20x when repeatedly querying a datset with genomic range filters. On a high coverage alignment dataset, this partitioning strategy improved latency from 1-2 minutes to 1-3 seconds when looking up genomic ranges.

Saving partitioned parquet files to disk

A GenomicRDD can be written to disk as a partitioned Parquet dataset with the GenomicRDD function saveAsPartitionedParquet. The optional partitionSize parameter defines the width in base pairs of the partitions within each contig.

A partitioned dataset can also be created from an input Parquet or SAM/BAM/CRAM file using the ADAM transformAlignments CLI, or Parquet/VCF files using the ADAM transformGenotypes CLI.

Loading partitioned parquet files

A GenomicRDD can be loaded from a partitioned Parquet dataset using the ADAMContext function loadPartitionedParquet[*] specific to each data type such as loadPartitionedParquetAlignments.

Layout of Partitioned Parquet directory

An ADAM partitioned Parquet dataset is written as a three level directory hierarchy. The outermost directory is the name of the dataset and contains metadata files as is found in unpartitioned ADAM Parquet datasets. Within the outer dataset directory, subdirectories are created with names based on the genomic contigs found in the dataset, for example a subdirectory will be named contigName=22 for chromosome 22. Within each contigName directory, there are subdirectories named using a computed value positionBin, for example a subdirectory named positionBin=5. Records from the dataset are written into Parquet files within the appropriate positionBin directory, computed based on the start position of the record using the calculation floor(start / partitionSize). For example, when using the default partitionSize of 1,000,000 base pairs, an alignment record with start position 20,100,000 on chromosome 22 would be found in a Parquet file at the path mydataset.adam/contigName=22/positionBin=20. The splitting of data into one or more Parquet fields in these leaf directories is automatic based on Parquet block size settings.

mySavedAdamDataset.adam
|
|-- _partitionedByStartPos
L-- contigName=1
    L-- positionBin=0
        |-- part-r-00001.parquet
        +-- part-r-00002.parquet
    L-- positionBin=1
        |-- part-r-00003.parquet
        |-- part-r-00004.parquet
    L-- positionBin= ( N bins ...)
L--  contigName= ( N contigs ... )
    |-- (N bins ... )

The existence of the file _partitionedByStartPos can be tested with the public function ADAMContext.isPartitioned(path) and can be used to determine explicitly if an ADAM Parquet dataset is partitioned using this scheme. The partition size which was used when the dataset was written to disk is stored in _partitionedByStartPos and is read in as a property of the dataset by the loadPartitionedParquet functions.

The Spark dataset API recognizes that the field positionBin is defined implicitly by the Parquet files’ partitioning scheme, and makes positionBin available as a field that can be queried through the Spark SQL API. positionBin is used internally by the public function GenomicRDD.filterByOverlappingRegions. User code in ADAM-shell or user applications could similarly utilize the positionBin field when creating Spark SQL queries on a genomicRDD.dataset backed by partitioned Parquet.

Re-using a previously loaded partitioned dataset:

When a partitioned dataset is first created within an ADAM session, a partition discovery/initialization step is performed that can take several minutes for large datasets. The original GenomicRDD object can then be re-used multiple times as the parent of different filtration and processing transformations and actions, without incurring this initializiation cost again. Thus, re-use of a parent partitioned GenomicRDD is key to realizing the latency advantages of partitioned datasets described above.

val mydata = loadPartitionedParquetAlignments("alignmets.adam")
val filteredCount1 = mydata.filterByOverlappingRegions(regions1).dataset.count
val filteredCount2 = mydata.filterByOverlappingRegions(regions2).dataset.count