util

case class IndexedFastaFile(sc: SparkContext, filePath: String, stringency: ValidationStringency = ValidationStringency.STRICT) extends ReferenceFile with Logging with Product with Serializable

Loads and extracts sequences directly from indexed fasta or fa files.
Loads and extracts sequences directly from indexed fasta or fa files. filePath requires fai index in the same directory with same naming convention.
filePath
path to fasta or fa index
class ParquetFileTraversable[T <: IndexedRecord] extends Traversable[T]

Implements a traversable collection that is backed by a Parquet file.
case class ReferenceContigMap(contigMap: Map[String, Seq[NucleotideContigFragment]]) extends ReferenceFile with Product with Serializable

A broadcastable ReferenceFile backed by a map containing contig name -> Seq[NucleotideContigFragment] pairs.
A broadcastable ReferenceFile backed by a map containing contig name -> Seq[NucleotideContigFragment] pairs.
contigMap
a map containing a Seq of contig fragments per contig.
class ReferenceContigMapSerializer extends Serializer[ReferenceContigMap]
trait ReferenceFile extends Serializable

File that contains a reference assembly that can be broadcasted
class TwoBitFile extends ReferenceFile

Represents a set of reference sequences backed by a .2bit file.
Represents a set of reference sequences backed by a .2bit file.
See http://genome.ucsc.edu/FAQ/FAQformat.html#format7 for the spec.
class TwoBitFileSerializer extends Serializer[TwoBitFile]

object AttributeUtils

AttributeUtils is a utility object for parsing optional fields from a BAM file, or the attributes column from an ADAM file.
object GenomeFileReader

Object for reading Bedtools genome files from disk.
Object for reading Bedtools genome files from disk. Also supports UCSC Genome Browser chromInfo files.
object ParquetLogger

Helper object for setting the logging level for Parquet.
object PhredUtils extends Serializable

Helper singleton for converting Phred scores to/from probabilities.
Helper singleton for converting Phred scores to/from probabilities.
As a reminder, given an error probability \epsilon, the Phred score q is:
q = -10 log_{10} \epsilon
object ReferenceContigMap extends Serializable

Companion object for creating a ReferenceContigMap from an RDD of contig fragments.
object SequenceDictionaryReader

Object for reading sequence dictionary files (.dict) from disk.
object TextRddWriter

Writes an RDD to disk as text and optionally merges.