package discount
Root package for the Discount k-mer counter.
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object
AllMinimizerFormats extends MinimizerFormats[DiscountConf]
Minimizer formats supported by Discount.
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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.