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. filePath requires fai index in the same directory with same naming convention.
- filePath
path to fasta or fa index
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new
IndexedFastaFile(sc: SparkContext, filePath: String, stringency: ValidationStringency = ValidationStringency.STRICT)
- filePath
path to fasta or fa index
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def
extract(region: ReferenceRegion): String
Extracts base sequence from FastaSequenceIndex
Extracts base sequence from FastaSequenceIndex
- region
The desired ReferenceRegion to extract.
- returns
The reference sequence at the desired locus.
- Definition Classes
- IndexedFastaFile → ReferenceFile
- val filePath: String
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val
references: SequenceDictionary
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- IndexedFastaFile → ReferenceFile
- val sc: SparkContext
- val stringency: ValidationStringency
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