Package org.broadinstitute.hellbender.tools.copynumber.datacollection

Class AllelicCountCollector

java.lang.Object

org.broadinstitute.hellbender.tools.copynumber.datacollection.AllelicCountCollector

public final class AllelicCountCollector
extends Object

Collects reference/alternate allele counts at specified sites. The alt count is defined as the total count minus the ref count, and the alt nucleotide is defined as the non-ref base with the highest count, with ties broken by the order of the bases in BASES.

Field Summary

Fields

Modifier and Type	Field	Description
static final List<Nucleotide>	BASES

Constructor Summary

Constructors

Constructor	Description
AllelicCountCollector(SampleLocatableMetadata metadata)

Method Summary

Modifier and Type	Method	Description
void	collectAtLocus(Nucleotide refBase, ReadPileup pileup, htsjdk.samtools.util.Locatable locus, int minBaseQuality)	Add counts to this class for a specific locus.
void	collectFromCollector(AllelicCountCollector allelicCountCollector)	Reminder that any additional information used through this method will not be able to enforce the minBaseQuality.
static AllelicCountCollector	combine(AllelicCountCollector allelicCountCollector1, AllelicCountCollector allelicCountCollector2, SampleLocatableMetadata sampleMetadata)	TODO: Docs and input parameter checking
AllelicCountCollection	getAllelicCounts()	Get the allelic counts gathered so far.

Methods inherited from class java.lang.Object

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

Field Details

BASES

public static final List<Nucleotide> BASES

Constructor Details

AllelicCountCollector

public AllelicCountCollector(SampleLocatableMetadata metadata)

Method Details

collectAtLocus

public void collectAtLocus(Nucleotide refBase,
 ReadPileup pileup,
 htsjdk.samtools.util.Locatable locus,
 int minBaseQuality)

Add counts to this class for a specific locus.

Parameters:

refBase - single nucleotide of the reference. Not null

pileup - associated pileup at the locus. Not null

locus - position in genome to collect alellic counts. Not null

minBaseQuality - minimum base quality in the read for that read to count at that position. Must be greater than or equal to 0.

getAllelicCounts

public AllelicCountCollection getAllelicCounts()

Get the allelic counts gathered so far.

Returns:

a reference to the AllelicCountCollection

collectFromCollector

public void collectFromCollector(AllelicCountCollector allelicCountCollector)

Reminder that any additional information used through this method will not be able to enforce the minBaseQuality.

Parameters:

allelicCountCollector - input data to combine with this.

combine

public static AllelicCountCollector combine(AllelicCountCollector allelicCountCollector1,
 AllelicCountCollector allelicCountCollector2,
 SampleLocatableMetadata sampleMetadata)

TODO: Docs and input parameter checking

Parameters:

allelicCountCollector1 -

allelicCountCollector2 -

Returns:

a new allelic count collector with the combined contents of the two inputs