Modifier and Type | Method and Description |
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Nucleobase |
NucleobaseAndReadFactory.createNucleobase(char genotype)
Create a Nucleobase object.
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Modifier and Type | Method and Description |
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java.util.ArrayList<Nucleobase> |
AbstractRead.getSequence()
Return the sequence of nucleobases from the reference genome which this Read object is a read of.
|
Modifier and Type | Method and Description |
---|---|
void |
CoverageStatisticsCalculator.updateRegionStatsFrom1Nucleobase(Nucleobase nucleobase)
Update the region coverage statistics from the coverage statistics for 1
nucleobase in that region.
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Modifier and Type | Method and Description |
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void |
NucleobaseAndReadFactory.createPairedEndReads(java.util.ArrayList<Nucleobase> leftEndSequence,
java.util.ArrayList<Nucleobase> rightEndSequence)
Create a pair of reads.
|
void |
NucleobaseAndReadFactory.createPairedEndReads(java.util.ArrayList<Nucleobase> leftEndSequence,
java.util.ArrayList<Nucleobase> rightEndSequence)
Create a pair of reads.
|
java.util.ArrayList<char[]> |
QualityScoreAndErrorGenerator.getQualityScoresAndGenotypesRead(boolean isLeft,
java.util.ArrayList<Nucleobase> nucleobases)
Get the encoded phred quality scores and the genotypes read.
|
void |
AbstractRead.setSequence(java.util.ArrayList<Nucleobase> sequence)
Set the sequence of nucleobases from the reference genome which this Read object is a read of.
|
Constructor and Description |
---|
Read(java.util.ArrayList<Nucleobase> sequence,
long uniqueID,
Read pairedEndRead,
boolean leftPEAndNeedsWriting,
char[] encodedQualityScores,
char[] genotypesThatAreRead,
int xCoordinate,
int yCoordinate)
Initialise a new Read object.
|