class Inputs extends AnyRef
A set of input files that can be parsed into com.jnpersson.discount.hash.InputFragment
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new
Inputs(files: Seq[String], k: Int, maxReadLength: Int)(implicit spark: SparkSession)
- files
files to read. A name of the format @list.txt will be parsed as a list of files.
- k
length of k-mers
- maxReadLength
max length of short sequences
- spark
the SparkSession
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val
conf: org.apache.hadoop.conf.Configuration
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def
forFile(file: String): InputReader
By looking at the file name and checking for the presence of a .fai file in the case of fasta, obtain an appropriate InputReader for a single file.
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final
def
getClass(): Class[_]
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def
getInputFragments(withRC: Boolean, withAmbiguous: Boolean = false): Dataset[InputFragment]
Parse all files in this set as InputFragments
Parse all files in this set as InputFragments
- withRC
whether to add reverse complement sequences
- withAmbiguous
whether to include ambiguous nucleotides. If not, the inputs will be split and only valid nucleotides retained.
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def
getSequenceTitles: Dataset[SeqTitle]
All sequence titles contained in this set of input files
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def
hashCode(): Int
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