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.

  • package fastdoop
  • 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.

  • 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.

  • package util

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

  • Frequency
  • Given
  • Lexicographic
  • MinimizerOrdering
  • Random
  • ReadSplitDemo
  • Signature
p

com.jnpersson

discount

package discount

Root package for this application.

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Type Members

  1. type Abundance = Long

    Internal type of abundance counts for k-mers.

    Internal type of abundance counts for k-mers. Even though this is is a Long, some algorithms use 32-bit values, so overall only 32-bit counters are currently supported, bounded by the two values below.

  2. sealed trait MinimizerOrdering extends AnyRef

    A type of ordering of a minimizer set

  3. type NTSeq = String

    Type of nucleotide sequences in human-readable form.

  4. type SeqID = Int

    Type of Sequence IDs

  5. type SeqLocation = Long

    Type of locations on sequences

  6. type SeqTitle = String

    Type of Sequence titles/headers (as read from fasta/fastq files)

Value Members

  1. def abundanceMax: Int

    Maximum value for abundance

  2. def abundanceMin: Int

    Minimum value for abundance

  3. object Frequency extends MinimizerOrdering with Product with Serializable

    Ordering by frequency (rare to common)

  4. object Given extends MinimizerOrdering with Product with Serializable

    A user-specified ordering

  5. object Lexicographic extends MinimizerOrdering with Product with Serializable

    Lexicographic (alphabetical) ordering

  6. object Random extends MinimizerOrdering with Product with Serializable

    Random ordering

  7. object ReadSplitDemo

    Minimal test program that demonstrates using the Discount API to split reads into super-mers without using Spark.

    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.

  8. object Signature extends MinimizerOrdering with Product with Serializable

    Ordering by minimizer signature, as in KMC2/3

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