package util
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Type Members
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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
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class
ParquetFileTraversable[T <: IndexedRecord] extends Traversable[T]
Implements a traversable collection that is backed by a Parquet file.
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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]
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trait
ReferenceFile extends Serializable
File that contains a reference assembly that can be broadcasted
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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]
Value Members
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object
ADAMShell
Utility methods for use in adam-shell.
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object
AttributeUtils
AttributeUtils is a utility object for parsing optional fields from a BAM file, or the attributes column from an ADAM file.
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object
FileExtensions
Match path names to file extensions.
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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.
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object
ParquetLogger
Helper object for setting the logging level for Parquet.
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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
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object
ReferenceContigMap extends Serializable
Companion object for creating a ReferenceContigMap from an RDD of contig fragments.
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object
SequenceDictionaryReader
Object for reading sequence dictionary files (.dict) from disk.
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object
TextRddWriter
Writes an RDD to disk as text and optionally merges.