Modifier and Type | Method and Description |
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Read |
Read.getPairedEndRead()
Get the read with which this read object forms a pair.
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Modifier and Type | Method and Description |
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java.util.ArrayList<Read> |
Nucleobase.getCoveringReads()
Get the list of covering reads - the reads which include this nucleobase.
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Modifier and Type | Method and Description |
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void |
Nucleobase.addCoveringRead(Read read)
Add a read to the list of reads which cover this nucleobase.
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void |
Read.setPairedEndRead(Read pairedEndRead)
Set the read with which this read object forms a pair.
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void |
Read.updateNucleobaseCoverage(Read read)
For each of the reference genome nucleobases in this read, add
the read into the nucleobase's covering reads ArrayList.
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Constructor and Description |
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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.
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