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

Methods inherited from interface 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