public class Read extends AbstractRead
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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Modifier and Type | Method and Description |
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java.lang.String |
getDebugString()
Get the debug string for this read object.
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Read |
getPairedEndRead()
Get the read with which this read object forms a pair.
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boolean |
isLeftReadAndNeedsWriting()
Get whether the Read object is a left read and needs writing.
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void |
setLeftReadAndNeedsWriting(boolean trueOrFalse)
Set whether the Read object is a left read and needs writing.
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void |
setPairedEndRead(Read pairedEndRead)
Set the read with which this read object forms a pair.
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java.lang.String |
toString()
Get the string that represents this read object.
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void |
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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getSequence, setSequence
public Read(java.util.ArrayList<Nucleobase> sequence, long uniqueID, Read pairedEndRead, boolean leftPEAndNeedsWriting, char[] encodedQualityScores, char[] genotypesThatAreRead, int xCoordinate, int yCoordinate)
sequence
- - the sequence of nucleobases in this read.uniqueID
- - the read's unique integer ID.pairedEndRead
- - the other read with which this one forms a pair.leftPEAndNeedsWriting
- - true if the read is a left read and needs writing, else false.encodedQualityScores
- - the encoded quality scores for this read.genotypesThatAreRead
- - the genotypes that get read.xCoordinate
- - the read's x-coordinate.yCoordinate
- - the read's y-coordinate.public void setLeftReadAndNeedsWriting(boolean trueOrFalse)
trueOrFalse
- - true if the read is a left read and needs writing, else false.public boolean isLeftReadAndNeedsWriting()
public Read getPairedEndRead()
public void setPairedEndRead(Read pairedEndRead)
pairedEndRead
- - the read with which this read forms a pair.public void updateNucleobaseCoverage(Read read)
read
- - this read.public java.lang.String toString()
toString
in class java.lang.Object
public java.lang.String getDebugString()