org.broadinstitute.hellbender.tools.walkers.contamination

Class ContaminationSegmenter

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationSegmenter

public class ContaminationSegmenter
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
static org.apache.commons.lang3.Range<java.lang.Double>	ALT_FRACTIONS_FOR_SEGMENTATION
static int	KERNEL_SEGMENTER_DIMENSION
static double	KERNEL_SEGMENTER_LINEAR_COST
static double	KERNEL_SEGMENTER_LOG_LINEAR_COST
static int	MAX_CHANGEPOINTS_PER_CHROMOSOME
static int	POINTS_PER_SEGMENTATION_WINDOW

Method Summary

Modifier and Type	Method and Description
static java.util.List<java.util.List<PileupSummary>>	findSegments(java.util.List<PileupSummary> sites) Partition the genome into segments of allelic copy number state using kernel segmentation of likely hets.

Methods inherited from class java.lang.Object

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

Field Detail

ALT_FRACTIONS_FOR_SEGMENTATION

public static final org.apache.commons.lang3.Range<java.lang.Double> ALT_FRACTIONS_FOR_SEGMENTATION

KERNEL_SEGMENTER_LINEAR_COST

public static final double KERNEL_SEGMENTER_LINEAR_COST

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Constant Field Values

KERNEL_SEGMENTER_LOG_LINEAR_COST

public static final double KERNEL_SEGMENTER_LOG_LINEAR_COST

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Constant Field Values

KERNEL_SEGMENTER_DIMENSION

public static final int KERNEL_SEGMENTER_DIMENSION

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Constant Field Values

POINTS_PER_SEGMENTATION_WINDOW

public static final int POINTS_PER_SEGMENTATION_WINDOW

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Constant Field Values

MAX_CHANGEPOINTS_PER_CHROMOSOME

public static final int MAX_CHANGEPOINTS_PER_CHROMOSOME

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Constant Field Values

Method Detail

findSegments

public static java.util.List<java.util.List<PileupSummary>> findSegments(java.util.List<PileupSummary> sites)

Partition the genome into segments of allelic copy number state using kernel segmentation of likely hets.

Parameters:

sites - a list of pileup summaries

Returns:

a list of segment intervals.