Package org.broadinstitute.hellbender.tools.walkers.coverage

Class DepthOfCoverageStats

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverageStats

public class DepthOfCoverageStats
extends Object

A class for storing summarized coverage statistics for DepthOfCoverage.

Constructor Summary

Constructors

Constructor	Description
DepthOfCoverageStats(int[] leftEndpoints, boolean includeDeletions, boolean dontComputeLocusTable)

Method Summary

Modifier and Type	Method	Description
Set<String>	getAllSamples()
double[]	getCoverageProportions(String sample)	Return a list of the cumulative depth counts as a perportion of total number of loci
int[]	getEndpoints()
Map<String,long[]>	getHistograms()
long[][]	getLocusCounts()
Map<String,Double>	getMeans()
long	getNumberOfLociCovered()	Returns a count of the number of loci summarized in this object
long	getTotalCoverage()
long	getTotalLoci()
double	getTotalMeanCoverage()
Map<String,Long>	getTotals()
void	merge(DepthOfCoverageStats newStats)
void	update(Map<String,int[]> countsBySample)
int	value2bin(int value)

Methods inherited from class java.lang.Object

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

Constructor Details

DepthOfCoverageStats

public DepthOfCoverageStats(int[] leftEndpoints,
 boolean includeDeletions,
 boolean dontComputeLocusTable)

Parameters:

leftEndpoints - Array of the left endpoints for desired coverage bins to track. See

includeDeletions - whether to count deletions at a site as coverage in the total

dontComputeLocusTable - if true then skip calculations for per-locus output tables

Method Details

update

public void update(Map<String,int[]> countsBySample)

merge

public void merge(DepthOfCoverageStats newStats)

getHistograms

public Map<String,long[]> getHistograms()

getLocusCounts

public long[][] getLocusCounts()

getEndpoints

public int[] getEndpoints()

getMeans

public Map<String,Double> getMeans()

getTotals

public Map<String,Long> getTotals()

getTotalLoci

public long getTotalLoci()

getAllSamples

public Set<String> getAllSamples()

Returns:

An unordered set of all the samples covered by this stats object

getTotalMeanCoverage

public double getTotalMeanCoverage()

getTotalCoverage

public long getTotalCoverage()

getCoverageProportions

public double[] getCoverageProportions(String sample)

Return a list of the cumulative depth counts as a perportion of total number of loci

Parameters:

sample -

Returns:

value2bin

public int value2bin(int value)

getNumberOfLociCovered

public long getNumberOfLociCovered()

Returns a count of the number of loci summarized in this object