public class Read extends AbstractRead
| 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.
|
| Modifier and Type | Method and Description |
|---|---|
java.lang.String |
getDebugString()
Get the debug string for this read object.
|
Read |
getPairedEndRead()
Get the read with which this read object forms a pair.
|
boolean |
isLeftReadAndNeedsWriting()
Get whether the Read object is a left read and needs writing.
|
void |
setLeftReadAndNeedsWriting(boolean trueOrFalse)
Set whether the Read object is a left read and needs writing.
|
void |
setPairedEndRead(Read pairedEndRead)
Set the read with which this read object forms a pair.
|
java.lang.String |
toString()
Get the string that represents this read object.
|
void |
updateNucleobaseCoverage(Read read)
For each of the reference genome nucleobases in this read, add
the read into the nucleobase's covering reads ArrayList.
|
getSequence, setSequencepublic 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.Objectpublic java.lang.String getDebugString()