Package ngs

Interface Pileup

All Superinterfaces:

PileupEvent, PileupEventIterator

All Known Subinterfaces:

PileupIterator

public interface Pileup
extends PileupEventIterator

Represents a slice through a stack of Alignments at a given position on the Reference

Field Summary

Fields inherited from interface ngs.PileupEvent

alignment_minus_strand, alignment_start, alignment_stop, deletion, insertion, insertion_before_deletion, insertion_before_match, insertion_before_mismatch, intron_minus, intron_plus, intron_unknown, match, mismatch, normal_indel, read_gap, read_overlap, replacement

Method Summary

Modifier and Type	Method	Description
int	getPileupDepth()	getPileupDepth
char	getReferenceBase()
long	getReferencePosition()	getReferencePosition
String	getReferenceSpec()	getReferenceSpec

Methods inherited from interface ngs.PileupEvent

getAlignmentBase, getAlignmentId, getAlignmentPosition, getAlignmentQuality, getEventIndelType, getEventRepeatCount, getEventType, getFirstAlignmentPosition, getInsertionBases, getInsertionQualities, getLastAlignmentPosition, getMappingQuality

Methods inherited from interface ngs.PileupEventIterator

nextPileupEvent, resetPileupEvent

Method Details

getReferenceSpec

String getReferenceSpec()
                 throws ErrorMsg

getReferenceSpec

Returns:

name of the Reference

Throws:

ErrorMsg - upon an error accessing data

getReferencePosition

long getReferencePosition()
                   throws ErrorMsg

getReferencePosition

Returns:

current position on the Reference

Throws:

ErrorMsg - upon an error accessing data

getReferenceBase

char getReferenceBase()
               throws ErrorMsg

Returns:

base at current Reference position

Throws:

ErrorMsg - upon an error accessing data

getPileupDepth

int getPileupDepth()
            throws ErrorMsg

getPileupDepth

Returns:

the coverage depth at the current reference position

Throws:

ErrorMsg - upon an error accessing data