public class OpticalDuplicateFinder extends ReadNameParser
Modifier and Type | Field | Description |
---|---|---|
static int |
DEFAULT_BIG_DUPLICATE_SET_SIZE |
|
static int |
DEFAULT_OPTICAL_DUPLICATE_DISTANCE |
|
int |
opticalDuplicatePixelDistance |
DEFAULT_READ_NAME_REGEX
Constructor | Description |
---|---|
OpticalDuplicateFinder() |
Uses the default duplicate distance and the default read name regex
ReadNameParser.DEFAULT_READ_NAME_REGEX . |
OpticalDuplicateFinder(String readNameRegex,
int opticalDuplicatePixelDistance,
htsjdk.samtools.util.Log log) |
Modifier and Type | Method | Description |
---|---|---|
boolean[] |
findOpticalDuplicates(List<? extends PhysicalLocation> list,
PhysicalLocation keeper) |
Finds which reads within the list of duplicates that are likely to be optical/co-localized duplicates of
one another.
|
void |
setBigDuplicateSetSize(int bigDuplicateSetSize) |
Sets the size of a set that is big enough to log progress about.
|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
addLocationInformation, getLastThreeFields, rapidParseInt
public int opticalDuplicatePixelDistance
public static final int DEFAULT_OPTICAL_DUPLICATE_DISTANCE
public static final int DEFAULT_BIG_DUPLICATE_SET_SIZE
public OpticalDuplicateFinder()
ReadNameParser.DEFAULT_READ_NAME_REGEX
.public OpticalDuplicateFinder(String readNameRegex, int opticalDuplicatePixelDistance, htsjdk.samtools.util.Log log)
readNameRegex
- see ReadNameParser.DEFAULT_READ_NAME_REGEX
.opticalDuplicatePixelDistance
- the optical duplicate pixel distancelog
- the log to which to write messages.public void setBigDuplicateSetSize(int bigDuplicateSetSize)
bigDuplicateSetSize
- the size of a set that is big enough to log progress aboutpublic boolean[] findOpticalDuplicates(List<? extends PhysicalLocation> list, PhysicalLocation keeper)
list
- a list of reads that are determined to be duplicates of one anotherkeeper
- a single PhysicalLocation that is the one being kept as non-duplicate, and thus should never be
annotated as an optical duplicate. May in some cases be null, or a PhysicalLocation not
contained within the list!