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