public class OpticalDuplicateFinder extends Object
Modifier and Type | Class and Description |
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static interface |
OpticalDuplicateFinder.PhysicalLocation
Small interface that provides access to the physical location information about a cluster.
|
Modifier and Type | Field and Description |
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static int |
DEFAULT_OPTICAL_DUPLICATE_DISTANCE |
static String |
DEFAULT_READ_NAME_REGEX |
int |
opticalDuplicatePixelDistance |
String |
readNameRegex |
Constructor and Description |
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OpticalDuplicateFinder() |
OpticalDuplicateFinder(int opticalDuplicatePixelDistance) |
OpticalDuplicateFinder(String readNameRegex) |
OpticalDuplicateFinder(String readNameRegex,
int opticalDuplicatePixelDistance) |
OpticalDuplicateFinder(String readNameRegex,
int opticalDuplicatePixelDistance,
Log log) |
Modifier and Type | Method and Description |
---|---|
boolean |
addLocationInformation(String readName,
OpticalDuplicateFinder.PhysicalLocation loc)
Method used to extract tile/x/y from the read name and add it to the PhysicalLocation so that it
can be used later to determine optical duplication
|
boolean[] |
findOpticalDuplicates(List<? extends OpticalDuplicateFinder.PhysicalLocation> list)
Finds which reads within the list of duplicates are likely to be optical duplicates of
one another.
|
public static final String DEFAULT_READ_NAME_REGEX
public static final int DEFAULT_OPTICAL_DUPLICATE_DISTANCE
public String readNameRegex
public int opticalDuplicatePixelDistance
public OpticalDuplicateFinder()
public OpticalDuplicateFinder(int opticalDuplicatePixelDistance)
public OpticalDuplicateFinder(String readNameRegex)
public OpticalDuplicateFinder(String readNameRegex, int opticalDuplicatePixelDistance)
public boolean addLocationInformation(String readName, OpticalDuplicateFinder.PhysicalLocation loc)
readName
- the name of the read/clusterloc
- the object to add tile/x/y topublic boolean[] findOpticalDuplicates(List<? extends OpticalDuplicateFinder.PhysicalLocation> list)
list
- a list of reads that are determined to be duplicates of one another