Packages

  • package root
    Definition Classes
    root
  • package com
    Definition Classes
    root
  • package jnpersson
    Definition Classes
    com
  • package discount

    Root package for this application.

    Root package for this application.

    Definition Classes
    jnpersson
  • package bucket

    Provides routines related to buckets/bins of k-mers.

    Provides routines related to buckets/bins of k-mers.

    Definition Classes
    discount
  • package fastdoop
    Definition Classes
    discount
  • package hash

    Provides classes for hashing k-mers and nucleotide sequences.

    Provides classes for hashing k-mers and nucleotide sequences. Hashing is done by identifying minimizers. Hashing all k-mers in a sequence thus corresponds to splitting the sequence into super-mers of length >= k (super k-mers) where all k-mers share the same minimizer.

    Definition Classes
    discount
  • package spark

    Provides classes and routines for running on Apache Spark.

    Provides classes and routines for running on Apache Spark. The main entry point is the Discount class. Once configured, it can be used to generate other classes of interest, such as GroupedSegments and CountedKmers.

    Definition Classes
    discount
  • package util

    Routines and classes for managing sequence and k-mer representations.

    Routines and classes for managing sequence and k-mer representations.

    Definition Classes
    discount
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  • ReadSplitDemo
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o

com.jnpersson.discount

ReadSplitDemo

object ReadSplitDemo

Minimal test program that demonstrates using the Discount API to split reads into super-mers without using Spark. Single-threaded, only works for FASTA files with unbroken reads. It is recommended to run on small input files so that the result can be inspected manually. In the output, the minimizer of each super-mer will be highlighted.

This tool makes use of the Discount configuration class CoreConf for convenience reasons. Note that this will ignore many arguments, for example the sample fraction (will always equal 1.0 as true sampling is not supported). However, in principle, all the minimizer orderings supported by Discount are supported. This tool ignores the following arguments: --long, --maxlen, --normalize, --numCPUs, --sample. Support for other arguments may be partial. Unlike the full Discount, only one file can be processed.

Run with e.g. the following command: sbt "runMain com.jnpersson.discount.ReadSplitDemo -m 10 -k 28 small.fasta"

To get help: sbt "runMain com.jnpersson.discount.ReadSplitDemo --help"

This tool is only a demo and currently ignores the following parameters: --maxlen, --normalize, --sample.

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  16. def prettyOutput(conf: ReadSplitConf): Unit
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  22. def writeToFile(conf: ReadSplitConf, destination: String): Unit

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