public class QualityScoreAndErrorGenerator
extends java.lang.Object
Modifier and Type | Field and Description |
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static char[] |
encodedSangerQualityScores |
Constructor and Description |
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QualityScoreAndErrorGenerator(int readLength,
boolean useRealQualityScores,
boolean simulateErrorInRead,
java.lang.String fastq1ForQualityScoresPath,
java.lang.String fastq2ForQualityScoresPath)
Initialise a new QualityScoreAndErrorGenerator object.
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Modifier and Type | Method and Description |
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long |
getNumACGTBasesCalled()
Get the number of ACGT bases.
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long |
getNumBaseCallErrors()
Get the number of base call errors that have been simulated.
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java.util.ArrayList<char[]> |
getQualityScoresAndGenotypesRead(boolean isLeft,
java.util.ArrayList<Nucleobase> nucleobases)
Get the encoded phred quality scores and the genotypes read.
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void |
resetNumBaseCallErrors()
Reset the number of simulated base call errors to 0.
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public QualityScoreAndErrorGenerator(int readLength, boolean useRealQualityScores, boolean simulateErrorInRead, java.lang.String fastq1ForQualityScoresPath, java.lang.String fastq2ForQualityScoresPath)
readLength
- - the length 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 java.util.ArrayList<char[]> getQualityScoresAndGenotypesRead(boolean isLeft, java.util.ArrayList<Nucleobase> nucleobases)
isLeft
- - true if the read is a left read, else false.nucleobases
- - human reference sequence nucleobases which the read is a read of.public long getNumBaseCallErrors()
public void resetNumBaseCallErrors()
public long getNumACGTBasesCalled()