Package ngs

# Interface PileupEvent

All Known Subinterfaces:
  `Pileup`, `PileupEventIterator`, `PileupIterator`

public interface PileupEvent
Represents a single cell of a sparse 2D matrix with Reference coordinates on one axis and stacked Alignments on the other axis

## Field Summary

Fields
Modifier and Type
Field
Description
`static final int`
`alignment_minus_strand`
`static final int`
`alignment_start`
`static final int`
`alignment_stop`
`static final int`
`deletion`
`static final int`
`insertion`
`static final int`
`insertion_before_deletion`
`static final int`
`insertion_before_match`
`static final int`
`insertion_before_mismatch`
`static final int`
`intron_minus`
`static final int`
`intron_plus`
`static final int`
`intron_unknown`
`static final int`
`match`
EventType
`static final int`
`mismatch`
`static final int`
`normal_indel`
EventIndelType
`static final int`
`read_gap`
`static final int`
`read_overlap`
`static final int`
`replacement`

## Method Summary

Modifier and Type
Method
Description
`char`
`getAlignmentBase()`
getAlignmentBase
`String`
`getAlignmentId()`
getAlignmentId
`long`
`getAlignmentPosition()`
getAlignmentPosition
`char`
`getAlignmentQuality()`
getAlignmentQuality
`int`
`getEventIndelType()`
getEventIndelType
`int`
`getEventRepeatCount()`
getEventRepeatCount
`int`
`getEventType()`
getEventType
`long`
`getFirstAlignmentPosition()`
getFirstAlignmentPosition
`String`
`getInsertionBases()`
getInsertionBases
`String`
`getInsertionQualities()`
getInsertionQualities
`long`
`getLastAlignmentPosition()`
getLastAlignmentPosition
`int`
`getMappingQuality()`
getMappingQuality

## Field Details

### match

static final int match
EventType

See Also:
  - Constant Field Values

### mismatch

static final int mismatch

See Also:
  - Constant Field Values

### deletion

static final int deletion

See Also:
  - Constant Field Values

### insertion

static final int insertion

See Also:
  - Constant Field Values

### insertion_before_match

static final int insertion_before_match

See Also:
  - Constant Field Values

### insertion_before_mismatch

static final int insertion_before_mismatch

See Also:
  - Constant Field Values

### insertion_before_deletion

static final int insertion_before_deletion

See Also:
  - Constant Field Values

### replacement

static final int replacement

See Also:
  - Constant Field Values

### alignment_start

static final int alignment_start

See Also:
  - Constant Field Values

### alignment_stop

static final int alignment_stop

See Also:
  - Constant Field Values

### alignment_minus_strand

static final int alignment_minus_strand

See Also:
  - Constant Field Values

### normal_indel

static final int normal_indel
EventIndelType

See Also:
  - Constant Field Values

### intron_plus

static final int intron_plus

See Also:
  - Constant Field Values

### intron_minus

static final int intron_minus

See Also:
  - Constant Field Values

### intron_unknown

static final int intron_unknown

See Also:
  - Constant Field Values

### read_overlap

static final int read_overlap

See Also:
  - Constant Field Values

### read_gap

static final int read_gap

See Also:
  - Constant Field Values

## Method Details

### getMappingQuality

int getMappingQuality() throws ErrorMsg
getMappingQuality

Returns:
  the mapping quality
Throws:
  `ErrorMsg` - upon an error accessing data

### getAlignmentId

String getAlignmentId() throws ErrorMsg
getAlignmentId

Returns:
  unique AlignmentId within ReadCollection
Throws:
  `ErrorMsg` - upon an error accessing data

### getAlignmentPosition

long getAlignmentPosition() throws ErrorMsg
getAlignmentPosition

Returns:
  Position of the alignment in Reference coordinates
Throws:
  `ErrorMsg` - upon an error accessing data

### getFirstAlignmentPosition

long getFirstAlignmentPosition() throws ErrorMsg
getFirstAlignmentPosition

Returns:
  the position of this Alignment's first event in Reference coordinates
Throws:
  `ErrorMsg` - upon an error accessing data

### getLastAlignmentPosition

long getLastAlignmentPosition() throws ErrorMsg
getLastAlignmentPosition

Returns:
  the position of this Alignment's last event in INCLUSIVE Reference coordinates
Throws:
  `ErrorMsg` - upon an error accessing data

### getEventType

int getEventType() throws ErrorMsg
getEventType

Returns:
  the type of event being represented
Throws:
  `ErrorMsg` - upon an error accessing data

### getAlignmentBase

char getAlignmentBase() throws ErrorMsg
getAlignmentBase

Returns:
  retrieves base aligned at current Reference position
Throws:
  `ErrorMsg` - if event is an insertion or deletion

### getAlignmentQuality

char getAlignmentQuality() throws ErrorMsg
getAlignmentQuality

Returns:
  retrieves base aligned at current Reference position
Throws:
  `ErrorMsg` - if event is an insertion or deletion

### getInsertionBases

String getInsertionBases() throws ErrorMsg
getInsertionBases

Returns:
  bases corresponding to insertion event
Throws:
  `ErrorMsg` - upon an error accessing data

### getInsertionQualities

String getInsertionQualities() throws ErrorMsg
getInsertionQualities

Returns:
  qualities corresponding to insertion event
Throws:
  `ErrorMsg` - upon an error accessing data

### getEventRepeatCount

int getEventRepeatCount() throws ErrorMsg
getEventRepeatCount

Returns:
  the number of times this event repeats, i.e. the distance to the first reference position yielding a different event type for this alignment
Throws:
  `ErrorMsg` - upon an error accessing data

### getEventIndelType

int getEventIndelType() throws ErrorMsg
getEventIndelType

Returns:
  detail about the type of indel when event type is an insertion or deletion
Throws:
  `ErrorMsg` - upon an error accessing data