umcg.genetica.io.pileup

Class PileupEntry

java.lang.Object

umcg.genetica.io.pileup.PileupEntry

public class PileupEntry
extends Object

Author:

Patrick Deelen

Constructor Summary

Constructors

Constructor and Description
PileupEntry(String chr, int pos, Allele refAllele, int readDepth, String basesString, int minimumBaseQuality) Only handles SNPs
PileupEntry(String chr, int pos, Allele refAllele, int readDepth, String basesString, String basesQualityString, int minimumBaseQuality)

Method Summary

Modifier and Type	Method and Description
gnu.trove.map.hash.TObjectDoubleHashMap<Allele>	getAlleleAverageQualities()
double	getAlleleAverageQuality(Allele allele)
int	getAlleleCount(Allele allele)
gnu.trove.map.hash.TObjectIntHashMap<Allele>	getAlleleCounts()
String	getChr()
int	getMinimumBaseQuality()
int	getPos()
int	getReadDepth()
Allele	getRefAllele()

Methods inherited from class java.lang.Object

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

Constructor Detail

PileupEntry

public PileupEntry(String chr,
                   int pos,
                   Allele refAllele,
                   int readDepth,
                   String basesString,
                   int minimumBaseQuality)
            throws PileupParseException

Only handles SNPs

Parameters:

chr -

pos -

refAllele -

readDepth -

basesString -

Throws:

PileupParseException

PileupEntry

public PileupEntry(String chr,
                   int pos,
                   Allele refAllele,
                   int readDepth,
                   String basesString,
                   String basesQualityString,
                   int minimumBaseQuality)
            throws PileupParseException

Throws:

PileupParseException

Method Detail

getChr

public String getChr()

getPos

public int getPos()

getRefAllele

public Allele getRefAllele()

getReadDepth

public int getReadDepth()

getAlleleCounts

public gnu.trove.map.hash.TObjectIntHashMap<Allele> getAlleleCounts()

getAlleleCount

public int getAlleleCount(Allele allele)

getAlleleAverageQualities

public gnu.trove.map.hash.TObjectDoubleHashMap<Allele> getAlleleAverageQualities()

getAlleleAverageQuality

public double getAlleleAverageQuality(Allele allele)

getMinimumBaseQuality

public int getMinimumBaseQuality()