picard.util.IntervalList

Enum IntervalListScatterMode

java.lang.Object

java.lang.Enum<IntervalListScatterMode>

picard.util.IntervalList.IntervalListScatterMode

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<IntervalListScatterMode>, org.broadinstitute.barclay.argparser.CommandLineParser.ClpEnum

public enum IntervalListScatterMode
extends java.lang.Enum<IntervalListScatterMode>
implements org.broadinstitute.barclay.argparser.CommandLineParser.ClpEnum

An enum to control the creation of the various IntervalListScatter objects

Enum Constant Summary

Enum Constants

Enum Constant and Description
BALANCING_WITHOUT_INTERVAL_SUBDIVISION A scatter approach that differs from INTERVAL_SUBDIVISION in a few ways.
BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW A scatter approach that differs from BALANCING_WITHOUT_INTERVAL_SUBDIVISION.
INTERVAL_COUNT A scatter by interval **count** which attempts to fill each resulting interval list with the same number of intervals, disregarding the base count.
INTERVAL_SUBDIVISION A simple scatter approach in which all output intervals have size equal to the total base count of the source list divide by the scatter count (except for possible variance in the final interval list).

Method Summary

Modifier and Type	Method and Description
java.lang.String	getHelpDoc()
IntervalListScatterer	make() Create the scatterer
static IntervalListScatterMode	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static IntervalListScatterMode[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

INTERVAL_SUBDIVISION

public static final IntervalListScatterMode INTERVAL_SUBDIVISION

A simple scatter approach in which all output intervals have size equal to the total base count of the source list divide by the scatter count (except for possible variance in the final interval list).

BALANCING_WITHOUT_INTERVAL_SUBDIVISION

public static final IntervalListScatterMode BALANCING_WITHOUT_INTERVAL_SUBDIVISION

A scatter approach that differs from INTERVAL_SUBDIVISION in a few ways.

1. No interval will be subdivided, and consequently, the requested scatter count is an upper bound of scatter count, not a guarantee as to how many IntervalLists will be produced (e.g., if scatterCount = 10 but there is only one input interval, only 1 interval list will be emitted).
2. When an interval would otherwise be split, it is instead deferred to the next scatter list.
3. The "target width" of each scatter list may be wider than what is computed for INTERVAL_SUBDIVISION. Specifically, if the widest interval in the source interval list is larger than what would otherwise be the target width, that interval's width is used.
   
   The reasoning for this is that this approach produces more consistently-sized interval lists, which is one of the objectives of scattering.

BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW

public static final IntervalListScatterMode BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW

A scatter approach that differs from BALANCING_WITHOUT_INTERVAL_SUBDIVISION.

1. We try to balance the number of unique bases in each interval list by estimating the remaining interval lists sizes. This is computed from the total number of unique bases and the bases we have consumed. This means that the interval list with the most number of unique bases is at most the ideal split length larger than the smallest interval list (unique # of bases).

INTERVAL_COUNT

public static final IntervalListScatterMode INTERVAL_COUNT

A scatter by interval **count** which attempts to fill each resulting interval list with the same number of intervals, disregarding the base count. This approach can be useful for tools that operate on the interval level rather than the base level, for example CNV calling.

Method Detail

values

public static IntervalListScatterMode[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (IntervalListScatterMode c : IntervalListScatterMode.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static IntervalListScatterMode valueOf(java.lang.String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

java.lang.IllegalArgumentException - if this enum type has no constant with the specified name

java.lang.NullPointerException - if the argument is null

getHelpDoc

public java.lang.String getHelpDoc()

Specified by:

getHelpDoc in interface org.broadinstitute.barclay.argparser.CommandLineParser.ClpEnum

make

public IntervalListScatterer make()

Create the scatterer

Returns:

a newly minted Scatterer