A B C D E F G H I L M N O Q R S T U

## G

generateArtificialFastqs(String) - Method in class artificialFastqGenerator.ArtificialFastqGenerator
  Main method for generating FASTQ files.
generateRandomDoubleBetween0And1() - Static method in class artificialFastqGenerator.ArtificialFastqGenerationUtils
  Generates a random double between 0 and 1.
generateToyGenome(String, int, boolean, int) - Static method in class artificialFastqGenerator.Genomes
  Generate a toy genome.
Genomes - Class in artificialFastqGenerator
  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.
Genomes() - Constructor for class artificialFastqGenerator.Genomes
getAlternateGenotypes(char) - Static method in class artificialFastqGenerator.ArtificialFastqGenerationUtils
  Return a char array containing the alternate genotypes.
getChromosomeStartEndStrs(String) - Static method in class artificialFastqGenerator.Genomes
  Get the human reference genome sequence start and end strings for a set of chromsomes.
getComplementGenotype() - Method in class artificialFastqGenerator.Nucleobase
  GEt the complement of the nucleobase's genotype.
getCoverage() - Method in class artificialFastqGenerator.Nucleobase
  Get the coverage for this nucleobase i.e.
getCoveringReads() - Method in class artificialFastqGenerator.Nucleobase
  Get the list of covering reads - the reads which include this nucleobase.
getDebugString() - Method in class artificialFastqGenerator.Read
  Get the debug string for this read object.
getGenotype() - Method in class artificialFastqGenerator.Nucleobase
  Get the nucleobase's genotype.
getNumACGTBasesCalled() - Method in class artificialFastqGenerator.NucleobaseAndReadFactory
  Get the number of ACGT nucleobases that have been called.
getNumACGTBasesCalled() - Method in class artificialFastqGenerator.QualityScoreAndErrorGenerator
  Get the number of ACGT bases.
getNumBaseCallErrors() - Method in class artificialFastqGenerator.NucleobaseAndReadFactory
  Get the number of base call errors that have been simulated.
getNumBaseCallErrors() - Method in class artificialFastqGenerator.QualityScoreAndErrorGenerator
  Get the number of base call errors that have been simulated.
getNumNucleobasesCreated() - Method in class artificialFastqGenerator.NucleobaseAndReadFactory
  Get the number of nucleobases that have been created.
getNumReadsCreated() - Method in class artificialFastqGenerator.NucleobaseAndReadFactory
  Get the number of reads that have been created.
getPairedEndRead() - Method in class artificialFastqGenerator.Read
  Get the read with which this read object forms a pair.
getQualityScoresAndGenotypesRead(boolean, ArrayList<Nucleobase>) - Method in class artificialFastqGenerator.QualityScoreAndErrorGenerator
  Get the encoded phred quality scores and the genotypes read.
getRandomIntWithinRange(int, double, int, int) - Static method in class artificialFastqGenerator.ArtificialFastqGenerationUtils
  Generates a pseudo-random number from a normal distribution, but with a minimum and maximum value.
getSequence() - Method in class artificialFastqGenerator.AbstractRead
  Return the sequence of nucleobases from the reference genome which this Read object is a read of.
getStackTraceString(Exception) - Static method in class artificialFastqGenerator.ArtificialFastqGenerationUtils
  Generate a stack trace string for an exception object.
getTargetCoverage() - Method in class artificialFastqGenerator.Nucleobase
  Get the target coverage for this nucleobase (the number of reads that we want to include this nucleobase).
getTargetCoverageViaGaussFuncOfGCcont(double, double, double, double, double) - Static method in class artificialFastqGenerator.ArtificialFastqGenerationUtils
  This method calculates a region's target coverage from its GC content.
getUniqueID() - Method in class artificialFastqGenerator.Nucleobase
  Get the nucleobase's unique integer ID.

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