org.broadinstitute.hellbender.utils.activityprofile

Class BandPassActivityProfile

java.lang.Object

org.broadinstitute.hellbender.utils.activityprofile.ActivityProfile

org.broadinstitute.hellbender.utils.activityprofile.BandPassActivityProfile

public class BandPassActivityProfile
extends ActivityProfile

A band pass filtering version of the activity profile Applies a band pass filter with a Gaussian kernel to the input state probabilities to smooth them out of an interval

Field Summary

Fields

Modifier and Type	Field and Description
static double	DEFAULT_SIGMA
static int	MAX_FILTER_SIZE

Fields inherited from class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfile

activeProbThreshold, contigLength, maxProbPropagationDistance, regionStartLoc, regionStopLoc, samHeader, stateList

Constructor Summary

Constructors

Constructor and Description
BandPassActivityProfile(int maxProbPropagationDistance, double activeProbThreshold, int maxFilterSize, double sigma, boolean adaptiveFilterSize, htsjdk.samtools.SAMFileHeader samHeader) Create an activity profile that implements a band pass filter on the states
BandPassActivityProfile(int maxProbPropagationDistance, double activeProbThreshold, int maxFilterSize, double sigma, htsjdk.samtools.SAMFileHeader samHeader) sets adaptiveFilterSize to true

Method Summary

Modifier and Type	Method and Description
protected static int	determineFilterSize(double[] kernel, double minProbToKeepInFilter)
int	getBandSize() Get the size (in bp) of the band pass filter
int	getFilteredSize() Get the filter size (which is the size of each wing of the band, minus the center point)
protected double[]	getKernel() Get the kernel of this band pass filter.
int	getMaxProbPropagationDistance() Our maximize propagation distance is whatever our parent's is, plus our filter size Stops the profile from interpreting sites that aren't yet fully determined due to propagation of the probabilities.
double	getSigma() Get the Gaussian kernel sigma value
protected static double[]	makeKernel(int filterSize, double sigma)
protected java.util.Collection<ActivityProfileState>	processState(ActivityProfileState justAddedState) Band pass the probabilities in the ActivityProfile, producing a new profile that's band pass filtered

Methods inherited from class org.broadinstitute.hellbender.utils.activityprofile.ActivityProfile

add, getContig, getEnd, getLocForOffset, getProbabilitiesAsArray, getSpan, getStateList, isEmpty, popReadyAssemblyRegions, size, toString

Methods inherited from class java.lang.Object

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

Field Detail

MAX_FILTER_SIZE

public static final int MAX_FILTER_SIZE

See Also:

Constant Field Values

DEFAULT_SIGMA

public static final double DEFAULT_SIGMA

See Also:

Constant Field Values

Constructor Detail

BandPassActivityProfile

public BandPassActivityProfile(int maxProbPropagationDistance,
                               double activeProbThreshold,
                               int maxFilterSize,
                               double sigma,
                               htsjdk.samtools.SAMFileHeader samHeader)

sets adaptiveFilterSize to true

BandPassActivityProfile

public BandPassActivityProfile(int maxProbPropagationDistance,
                               double activeProbThreshold,
                               int maxFilterSize,
                               double sigma,
                               boolean adaptiveFilterSize,
                               htsjdk.samtools.SAMFileHeader samHeader)

Create an activity profile that implements a band pass filter on the states

Parameters:

maxProbPropagationDistance - region probability propagation distance beyond it's maximum size

activeProbThreshold - threshold for the probability of a profile state being active

maxFilterSize - the maximum size of the band pass filter we are allowed to create, regardless of sigma

sigma - the variance of the Gaussian kernel for this band pass filter

adaptiveFilterSize - if true, use the kernel itself to determine the best filter size

Method Detail

determineFilterSize

protected static int determineFilterSize(double[] kernel,
                                         double minProbToKeepInFilter)

makeKernel

protected static double[] makeKernel(int filterSize,
                                     double sigma)

getMaxProbPropagationDistance

public int getMaxProbPropagationDistance()

Our maximize propagation distance is whatever our parent's is, plus our filter size Stops the profile from interpreting sites that aren't yet fully determined due to propagation of the probabilities.

Overrides:

getMaxProbPropagationDistance in class ActivityProfile

Returns:

the distance in bp we might move our probabilities around for some site i

getBandSize

public int getBandSize()

Get the size (in bp) of the band pass filter

Returns:

a positive integer

getFilteredSize

public int getFilteredSize()

Get the filter size (which is the size of each wing of the band, minus the center point)

Returns:

a positive integer

getSigma

public double getSigma()

Get the Gaussian kernel sigma value

Returns:

a positive double

getKernel

protected double[] getKernel()

Get the kernel of this band pass filter. Do not modify returned result

Returns:

the kernel used in this band pass filter

processState

protected java.util.Collection<ActivityProfileState> processState(ActivityProfileState justAddedState)

Band pass the probabilities in the ActivityProfile, producing a new profile that's band pass filtered

Overrides:

processState in class ActivityProfile

Parameters:

justAddedState - the state our client provided to use to add to the list

Returns:

a new double[] that's the band-pass filtered version of this profile