public class NucleobaseAndReadFactory
extends java.lang.Object
Constructor and Description |
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NucleobaseAndReadFactory(int startingXCoord,
int startingYCoord,
int readLength,
boolean useRealQualityScores,
boolean simulateErrorInRead,
java.lang.String fastq1ForQualityScoresPath,
java.lang.String fastq2ForQualityScoresPath)
Initialises a new NucleobaseAndReadFactory object.
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Modifier and Type | Method and Description |
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Nucleobase |
createNucleobase(char genotype)
Create a Nucleobase object.
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void |
createPairedEndReads(java.util.ArrayList<Nucleobase> leftEndSequence,
java.util.ArrayList<Nucleobase> rightEndSequence)
Create a pair of reads.
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long |
getNumACGTBasesCalled()
Get the number of ACGT nucleobases that have been called.
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long |
getNumBaseCallErrors()
Get the number of base call errors that have been simulated.
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long |
getNumNucleobasesCreated()
Get the number of nucleobases that have been created.
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long |
getNumReadsCreated()
Get the number of reads that have been created.
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void |
logOverallErrorStats()
Log the overall error statistics.
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void |
resetFieldsForNewChromosome()
Reset fields ready to process a new chromosome.
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public NucleobaseAndReadFactory(int startingXCoord, int startingYCoord, int readLength, boolean useRealQualityScores, boolean simulateErrorInRead, java.lang.String fastq1ForQualityScoresPath, java.lang.String fastq2ForQualityScoresPath)
startingXCoord
- - the starting X coordinate.startingYCoord
- - the starting Y coordinate.readLength
- - the lenght of each read.useRealQualityScores
- - true if using quality scores from an existing fastq file, else false.simulateErrorInRead
- - true if simulating error in reads, else false.fastq1ForQualityScoresPath
- - the 1st fastq file whose quality scores are used.fastq2ForQualityScoresPath
- - the 2nd fastq file whose quality scores are used.public Nucleobase createNucleobase(char genotype)
genotype
- - the nucleobase's genotype.public void createPairedEndReads(java.util.ArrayList<Nucleobase> leftEndSequence, java.util.ArrayList<Nucleobase> rightEndSequence)
leftEndSequence
- - the sequence of nucleobases for the left read.rightEndSequence
- - the sequence of nucleobases for the right read.public long getNumNucleobasesCreated()
public long getNumReadsCreated()
public long getNumBaseCallErrors()
public long getNumACGTBasesCalled()
public void logOverallErrorStats()
public void resetFieldsForNewChromosome()