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class CountedKmers extends AnyRef

Routines for converting encoded super-mers into individual counted k-mers.

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Instance Constructors

  1. new CountedKmers(buckets: Dataset[ReducibleBucket], orientation: Orientation, splitter: Broadcast[AnyMinSplitter])(implicit spark: SparkSession)

    buckets

    Super-mer buckets

    orientation

    orientation filter for k-mers

    splitter

    Splitter for constructing super-mers

    spark

    the Spark session

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  14. def supermersWithTags: Dataset[(BucketId, NTBitArray, Array[Int])]

    Obtain these counts as triplets of (minimizer, encoded super-mer, tags for super-mer)

  15. def supermersWithTagsReadable(withZeroTags: Boolean): Dataset[(NTSeq, NTSeq, String)]

    Obtain these counts as human-readable triplets of (minimizer, super-mer, tags for super-mer

    Obtain these counts as human-readable triplets of (minimizer, super-mer, tags for super-mer

    withZeroTags

    whether to include k-mers with zero tags (counts). If false, super-mers will be split as required. Even if true, empty super-mers (purely zero tags) will not be included.

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  21. def withSequences: Dataset[(NTSeq, Abundance)]

    Obtain these counts as pairs of k-mer sequence strings and abundances.

  22. def writeFasta(output: String): Unit

    Write counted k-mers with sequences as FASTA files to HDFS.

    Write counted k-mers with sequences as FASTA files to HDFS. The count will be used as the sequence ID of each k-mer. This action triggers a computation.

    output

    Directory to write to (prefix name)

  23. def writeSupermersFasta(output: String, withZero: Boolean, identifier: String): Unit

    Output super-mers as FASTA.

    Output super-mers as FASTA. Triggers a computation. Headers will contain identifier, minimizer, and count of every k-mer.

    output

    directory to write to (prefix name)

    withZero

    include zero k-mers (gaps)

    identifier

    FASTA identifier of every sequence

  24. def writeSupermersTSV(output: String, withZero: Boolean): Unit

    Output super-mers as TSV.

    Output super-mers as TSV. Triggers a computation. The resulting file will contain minimizer, super-mer, and count of every k-mer.

    output

    directory to write to (prefix name)

    withZero

    output zero k-mers (gaps)

  25. def writeTSV(output: String): Unit

    Write a table as TSV.

    Write a table as TSV. This action triggers a computation.

    output

    Directory to write to (prefix name)

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