package discount
Root package for this application.
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Type Members
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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.
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sealed
trait
MinimizerOrdering extends AnyRef
A type of ordering of a minimizer set
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type
NTSeq = String
Type of nucleotide sequences in human-readable form.
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type
SeqID = Int
Type of Sequence IDs
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type
SeqLocation = Long
Type of locations on sequences
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type
SeqTitle = String
Type of Sequence titles/headers (as read from fasta/fastq files)
Value Members
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def
abundanceMax: Int
Maximum value for abundance
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def
abundanceMin: Int
Minimum value for abundance
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object
Frequency extends MinimizerOrdering with Product with Serializable
Ordering by frequency (rare to common)
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object
Given extends MinimizerOrdering with Product with Serializable
A user-specified ordering
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object
Lexicographic extends MinimizerOrdering with Product with Serializable
Lexicographic (alphabetical) ordering
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object
Random extends MinimizerOrdering with Product with Serializable
Random ordering
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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.
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object
Signature extends MinimizerOrdering with Product with Serializable
Ordering by minimizer signature, as in KMC2/3