Class | Description |
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AbstractRead | |
ArtificialFastqGenerationUtils |
ArtificialFastqGenerationUtils consists exclusively of static utility methods that are used in
artificial fastq generation.
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ArtificialFastqGenerator |
An instance of this class can be used to generate artificial FASTQ files from the human reference genome.
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BriefLogFormatter |
Instances of this class can log messages which consist of the time followed by the record.
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CoverageStatisticsCalculator |
Instances of this class calculate regional and overall coverage statistics for nucleobases.
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Genomes |
The Genomes class provides facilities for (1) creating a toy genome, (2) getting the start and end strings for a
chromosome in the human reference genome, (3) analysing and producing summary statistics for the human reference genome.
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Main |
This class is responsible for checking whether the user's command is valid,
and if it is, creating instances of the ArtificialFastqGenerator class in order
to generate fastq files.
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Nucleobase |
An instance of the Nucleobase class corresponds to a nucleobase in the human reference genome.
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NucleobaseAndReadFactory |
An instance of this class can be used to create new Nucleobase and Read objects.
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QualityScoreAndErrorGenerator |
An instance of this class can be used to generate (1) ASCII encodings of Phred quality scores for bases in reads; (2)
base-call errors.
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Read |
An instance of this class corresponds to a read in an artificial fastq file.
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