PileupIterator

All Superinterfaces:: Pileup, PileupEvent, PileupEventIterator

public interface PileupIterator extends Pileup

Iterates across a list of Pileups

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

boolean

nextPileup()

Advance to first Pileup on initial invocation advance to next Pileup subsequently

Methods inherited from interface Pileup
getPileupDepth, getReferenceBase, getReferencePosition, 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
- nextPileup
  
  boolean nextPileup() throws ErrorMsg
  
  Advance to first Pileup on initial invocation advance to next Pileup subsequently
  
  Returns:
  
  false if no more Pileups are available.
  
  Throws:
  
  ErrorMsg - if more Pileups should be available, but could not be accessed.