class FastqShortInput extends InputReader
Input reader for FASTQ short reads. Uses FASTQInputFileFormat
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new
FastqShortInput(file: String, k: Int, maxReadLength: Int)(implicit spark: SparkSession)
- file
the file to read
- k
length of k-mers
- maxReadLength
maximum length of a single read
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val
conf: org.apache.hadoop.conf.Configuration
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def
getFragments(): RDD[InputFragment]
Read sequence data as fragments from the input files, removing any newlines.
Read sequence data as fragments from the input files, removing any newlines.
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- FastqShortInput → InputReader
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def
getInputFragments(withRC: Boolean, withAmbiguous: Boolean): Dataset[InputFragment]
Load sequence fragments from files, optionally adding reverse complements and/or sampling.
Load sequence fragments from files, optionally adding reverse complements and/or sampling.
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- InputReader
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def
getSequenceTitles: Dataset[SeqTitle]
Sequence titles in this file
Sequence titles in this file
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val
sc: SparkContext
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