Package picard.illumina.parser
Class ClusterData
- java.lang.Object
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- picard.illumina.parser.ClusterData
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public class ClusterData extends Object
Store the information from Illumina files for a single cluster with one or more reads.
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Constructor Summary
Constructors Constructor Description ClusterData(ReadData... reads)
Used for testing, reads is set directly with no copying to the input arrayClusterData(ReadType[] readTypes)
Creates a ClusterData with one read for each type provided
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
getLane()
String
getMatchedBarcode()
int
getNumReads()
ReadData
getRead(int index)
int
getTile()
int
getX()
int
getY()
Boolean
isPf()
boolean
laneIsSet()
void
setLane(int lane)
void
setMatchedBarcode(String matchedBarcode)
void
setOrCheckLane(int lane)
Either set this value if not already set, or if already set, throw an exception if new value != current value.void
setOrCheckPf(boolean pf)
Either set this value if not already set, or if already set, throw an exception if new value != current value.void
setOrCheckTile(int tile)
Either set this value if not already set, or if already set, throw an exception if new value != current value.void
setOrCheckX(int x)
Either set this value if not already set, or if already set, throw an exception if new value != current value.void
setOrCheckY(int y)
Either set this value if not already set, or if already set, throw an exception if new value != current value.void
setPf(boolean pf)
void
setTile(int tile)
void
setX(int x)
void
setY(int y)
boolean
tileIsSet()
String
toString()
boolean
xIsSet()
boolean
yIsSet()
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Method Detail
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getTile
public int getTile()
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setTile
public void setTile(int tile)
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tileIsSet
public boolean tileIsSet()
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getRead
public ReadData getRead(int index)
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getNumReads
public int getNumReads()
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setOrCheckTile
public void setOrCheckTile(int tile)
Either set this value if not already set, or if already set, throw an exception if new value != current value.
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getLane
public int getLane()
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setLane
public void setLane(int lane)
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laneIsSet
public boolean laneIsSet()
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setOrCheckLane
public void setOrCheckLane(int lane)
Either set this value if not already set, or if already set, throw an exception if new value != current value.
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getX
public int getX()
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setX
public void setX(int x)
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xIsSet
public boolean xIsSet()
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setOrCheckX
public void setOrCheckX(int x)
Either set this value if not already set, or if already set, throw an exception if new value != current value.
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getY
public int getY()
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setY
public void setY(int y)
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yIsSet
public boolean yIsSet()
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setOrCheckY
public void setOrCheckY(int y)
Either set this value if not already set, or if already set, throw an exception if new value != current value.
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isPf
public Boolean isPf()
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setPf
public void setPf(boolean pf)
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setOrCheckPf
public void setOrCheckPf(boolean pf)
Either set this value if not already set, or if already set, throw an exception if new value != current value.
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getMatchedBarcode
public String getMatchedBarcode()
- Returns:
- The barcode matched (not the actual sequence from the read, which may not perfectly match the barcode).
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setMatchedBarcode
public void setMatchedBarcode(String matchedBarcode)
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