picard.util.IntervalList

Class IntervalListScattererByIntervalCount

java.lang.Object

picard.util.IntervalList.IntervalListScattererByIntervalCount

All Implemented Interfaces:

IntervalListScatterer

public class IntervalListScattererByIntervalCount
extends java.lang.Object
implements IntervalListScatterer

Scatters IntervalList by interval count so that resulting IntervalList's have the same number of intervals in them. An exception is made for the final interval list, which will always contain at least this number of intervals, but may also contain the remainder.

Constructor Summary

Constructors

Constructor and Description
IntervalListScattererByIntervalCount()

Method Summary

Modifier and Type	Method and Description
int	deduceIdealSplitWeight(htsjdk.samtools.util.IntervalList intervalList, int nCount) A method that determines the ideal target "weight" of the output IntervalList.
long	intervalWeight(htsjdk.samtools.util.Interval interval) A method that defines the "weight" of an interval list for the purpose of scattering.
long	listWeight(htsjdk.samtools.util.IntervalList intervalList) A method that defines the "weight" of an interval for the purpose of scattering.
java.util.List<htsjdk.samtools.util.Interval>	takeSome(htsjdk.samtools.util.Interval interval, long idealSplitWeight, long currentSize, double projectSizeOfRemaining) 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 java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface picard.util.IntervalList.IntervalListScatterer

preprocessIntervalList, scatter

Constructor Detail

IntervalListScattererByIntervalCount

public IntervalListScattererByIntervalCount()

Method Detail

intervalWeight

public long intervalWeight(htsjdk.samtools.util.Interval interval)

Description copied from interface: IntervalListScatterer

A method that defines the "weight" of an interval list for the purpose of scattering. The class will attempt to create sublists that all have similar weights.

Specified by:

intervalWeight in interface IntervalListScatterer

listWeight

public long listWeight(htsjdk.samtools.util.IntervalList intervalList)

Description copied from interface: IntervalListScatterer

A method that defines the "weight" of an interval for the purpose of scattering. The class will attempt to create sublists that all have similar weights. This method need to estimate the change in any sublists weight due to the possible of the provided interval.

Specified by:

listWeight in interface IntervalListScatterer

takeSome

public java.util.List<htsjdk.samtools.util.Interval> takeSome(htsjdk.samtools.util.Interval interval,
                                                              long idealSplitWeight,
                                                              long currentSize,
                                                              double projectSizeOfRemaining)

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.

Specified by:

takeSome in interface IntervalListScatterer

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.

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 interface IntervalListScatterer

Parameters:

intervalList - the IntervalList that is about to get split

nCount - the scatter count into which to split intervalList

Returns:

The ideal "weight" of the output IntervalList's