artificialFastqGenerator
Date: 2014-10-01

# Package artificialFastqGenerator

- Class Summary
  Class | Description
  --- | ---
  AbstractRead |
  ArtificialFastqGenerationUtils | ArtificialFastqGenerationUtils consists exclusively of static utility methods that are used in artificial fastq generation.
  ArtificialFastqGenerator | An instance of this class can be used to generate artificial FASTQ files from the human reference genome.
  BriefLogFormatter | Instances of this class can log messages which consist of the time followed by the record.
  CoverageStatisticsCalculator | Instances of this class calculate regional and overall coverage statistics for nucleobases.
  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.
  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.
  Nucleobase | An instance of the Nucleobase class corresponds to a nucleobase in the human reference genome.
  NucleobaseAndReadFactory | An instance of this class can be used to create new Nucleobase and Read objects.
  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.
  Read | An instance of this class corresponds to a read in an artificial fastq file.