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