Package picard.util.IntervalList
Class IntervalListScattererWithoutSubdivision
java.lang.Object
picard.util.IntervalList.IntervalListScattererByBaseCount
picard.util.IntervalList.IntervalListScattererWithoutSubdivision
- All Implemented Interfaces:
IntervalListScatterer
- Direct Known Subclasses:
IntervalListScattererWithoutSubdivisionWithOverflow
A BaseCount Scatterer that avoid breaking-up intervals. This is done by by only adding intervals to the current list if
the resulting size no larger than the "ideal" size. In addition, the ideal length will not be small than the largest sub-interval
in the input list.
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionint
deduceIdealSplitWeight
(htsjdk.samtools.util.IntervalList intervalList, int nCount) A method that determines the ideal target "weight" of the output IntervalList.protected boolean
shouldIncludeInterval
(long idealSplitWeight, double projectedSizeOfRemaining, long projectedSize) List
<htsjdk.samtools.util.Interval> takeSome
(htsjdk.samtools.util.Interval interval, long idealSplitWeight, long currentSize, double projectedSizeOfRemaining) Figure out how much of the input interval to put into current list and how much to leave for the next interval list.Methods inherited from class picard.util.IntervalList.IntervalListScattererByBaseCount
intervalWeight, listWeight
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface picard.util.IntervalList.IntervalListScatterer
preprocessIntervalList, scatter
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Constructor Details
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IntervalListScattererWithoutSubdivision
public IntervalListScattererWithoutSubdivision()
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Method Details
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takeSome
public List<htsjdk.samtools.util.Interval> takeSome(htsjdk.samtools.util.Interval interval, long idealSplitWeight, long currentSize, double projectedSizeOfRemaining) Description copied from interface:IntervalListScatterer
Figure out how much of the input interval to put into current list and how much to leave for the next interval list.- Parameters:
interval
-- Returns:
- a list of two (possibly null) elements. The first element should be added to the current interval list, the second should be offered to the next interval list.
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shouldIncludeInterval
protected boolean shouldIncludeInterval(long idealSplitWeight, double projectedSizeOfRemaining, long projectedSize) -
deduceIdealSplitWeight
public int deduceIdealSplitWeight(htsjdk.samtools.util.IntervalList intervalList, int nCount) Description copied from interface:IntervalListScatterer
A method that determines the ideal target "weight" of the output IntervalList.- Specified by:
deduceIdealSplitWeight
in interfaceIntervalListScatterer
- Overrides:
deduceIdealSplitWeight
in classIntervalListScattererByBaseCount
- Parameters:
intervalList
- theIntervalList
that is about to get splitnCount
- the scatter count into which to split intervalList- Returns:
- The ideal "weight" of the output
IntervalList
's
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