org.broadinstitute.hellbender.utils.activityprofile

Class ActivityProfileState

java.lang.Object

org.broadinstitute.hellbender.utils.activityprofile.ActivityProfileState

public final class ActivityProfileState
extends java.lang.Object

Captures the probability that a specific locus in the genome represents an "active" site containing real variation.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ActivityProfileState.Type The type of the value returned by getResultValue()

Constructor Summary

Constructors

Constructor and Description
ActivityProfileState(SimpleInterval loc, double activeProb) Create a new ActivityProfileState at loc with probability of being active of activeProb
ActivityProfileState(SimpleInterval loc, double activeProb, ActivityProfileState.Type resultState, java.lang.Number resultValue) Create a new ActivityProfileState at loc with probability of being active of activeProb that maintains some information about the result state and value The only state value in use is HIGH_QUALITY_SOFT_CLIPS, and here the value is interpreted as the number of bp affected by the soft clips.

Method Summary

Modifier and Type	Method and Description
SimpleInterval	getLoc() Get the locus associated with the ActivityProfileState
int	getOffset(htsjdk.samtools.util.Locatable regionStartLoc) The offset of state w.r.t.
ActivityProfileState.Type	getResultState()
java.lang.Number	getResultValue()
double	isActiveProb()
void	setIsActiveProb(double activeProb) Set the probability that this site is active.
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

ActivityProfileState

public ActivityProfileState(SimpleInterval loc,
                            double activeProb)

Create a new ActivityProfileState at loc with probability of being active of activeProb

Parameters:

loc - the position of the result profile (for debugging purposes)

activeProb - the probability of being active (between 0 and 1)

ActivityProfileState

public ActivityProfileState(SimpleInterval loc,
                            double activeProb,
                            ActivityProfileState.Type resultState,
                            java.lang.Number resultValue)

Create a new ActivityProfileState at loc with probability of being active of activeProb that maintains some information about the result state and value The only state value in use is HIGH_QUALITY_SOFT_CLIPS, and here the value is interpreted as the number of bp affected by the soft clips.

Parameters:

loc - the position of the result profile (for debugging purposes)

activeProb - the probability of being active (between 0 and 1)

Method Detail

isActiveProb

public double isActiveProb()

setIsActiveProb

public void setIsActiveProb(double activeProb)

Set the probability that this site is active. Probabilities should be between 0.0 and 1.0, however this is not currently enforced because the BandPassActivityProfile can sometimes generate probabilities that slightly exceed 1.0 when moving probability mass around. We intend to fix this by capping at 1.0, but first we must evaluate the effects of capping on the HaplotypeCaller.

Parameters:

activeProb - probability (should be between 0.0 and 1.0) that the site is active

getResultState

public ActivityProfileState.Type getResultState()

Returns:

The type of the value returned by getResultValue()

getResultValue

public java.lang.Number getResultValue()

Returns:

Numeric value associated with getResultState(). If getResultState() is HIGH_QUALITY_SOFT_CLIPS, this is the number of bp affected by the soft clips

getOffset

public int getOffset(htsjdk.samtools.util.Locatable regionStartLoc)

The offset of state w.r.t. our current region's start location

Parameters:

regionStartLoc - the start of the region, as a Locatable

Returns:

the position of this profile relative to the start of this region

getLoc

public SimpleInterval getLoc()

Get the locus associated with the ActivityProfileState

Returns:

the locus associated with the ActivityProfileState as a SimpleInterval

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object