Package ngs
Interface PileupEvent
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- 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
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Field Summary
Fields Modifier and Type Field Description static int
alignment_minus_strand
static int
alignment_start
static int
alignment_stop
static int
deletion
static int
insertion
static int
insertion_before_deletion
static int
insertion_before_match
static int
insertion_before_mismatch
static int
intron_minus
static int
intron_plus
static int
intron_unknown
static int
match
EventTypestatic int
mismatch
static int
normal_indel
EventIndelTypestatic int
read_gap
static int
read_overlap
static int
replacement
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description char
getAlignmentBase()
getAlignmentBasejava.lang.String
getAlignmentId()
getAlignmentIdlong
getAlignmentPosition()
getAlignmentPositionchar
getAlignmentQuality()
getAlignmentQualityint
getEventIndelType()
getEventIndelTypeint
getEventRepeatCount()
getEventRepeatCountint
getEventType()
getEventTypelong
getFirstAlignmentPosition()
getFirstAlignmentPositionjava.lang.String
getInsertionBases()
getInsertionBasesjava.lang.String
getInsertionQualities()
getInsertionQualitieslong
getLastAlignmentPosition()
getLastAlignmentPositionint
getMappingQuality()
getMappingQuality
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Field Detail
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match
static final int match
EventType- See Also:
- Constant Field Values
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mismatch
static final int mismatch
- See Also:
- Constant Field Values
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deletion
static final int deletion
- See Also:
- Constant Field Values
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insertion
static final int insertion
- See Also:
- Constant Field Values
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insertion_before_match
static final int insertion_before_match
- See Also:
- Constant Field Values
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insertion_before_mismatch
static final int insertion_before_mismatch
- See Also:
- Constant Field Values
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insertion_before_deletion
static final int insertion_before_deletion
- See Also:
- Constant Field Values
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replacement
static final int replacement
- See Also:
- Constant Field Values
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alignment_start
static final int alignment_start
- See Also:
- Constant Field Values
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alignment_stop
static final int alignment_stop
- See Also:
- Constant Field Values
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alignment_minus_strand
static final int alignment_minus_strand
- See Also:
- Constant Field Values
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normal_indel
static final int normal_indel
EventIndelType- See Also:
- Constant Field Values
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intron_plus
static final int intron_plus
- See Also:
- Constant Field Values
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intron_minus
static final int intron_minus
- See Also:
- Constant Field Values
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intron_unknown
static final int intron_unknown
- See Also:
- Constant Field Values
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read_overlap
static final int read_overlap
- See Also:
- Constant Field Values
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read_gap
static final int read_gap
- See Also:
- Constant Field Values
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Method Detail
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getMappingQuality
int getMappingQuality() throws ErrorMsg
getMappingQuality- Returns:
- the mapping quality
- Throws:
ErrorMsg
- upon an error accessing data
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getAlignmentId
java.lang.String getAlignmentId() throws ErrorMsg
getAlignmentId- Returns:
- unique AlignmentId within ReadCollection
- Throws:
ErrorMsg
- upon an error accessing data
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getAlignmentPosition
long getAlignmentPosition() throws ErrorMsg
getAlignmentPosition- Returns:
- Position of the alignment in Reference coordinates
- Throws:
ErrorMsg
- upon an error accessing data
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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
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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
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getEventType
int getEventType() throws ErrorMsg
getEventType- Returns:
- the type of event being represented
- Throws:
ErrorMsg
- upon an error accessing data
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getAlignmentBase
char getAlignmentBase() throws ErrorMsg
getAlignmentBase- Returns:
- retrieves base aligned at current Reference position
- Throws:
ErrorMsg
- if event is an insertion or deletion
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getAlignmentQuality
char getAlignmentQuality() throws ErrorMsg
getAlignmentQuality- Returns:
- retrieves base aligned at current Reference position
- Throws:
ErrorMsg
- if event is an insertion or deletion
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getInsertionBases
java.lang.String getInsertionBases() throws ErrorMsg
getInsertionBases- Returns:
- bases corresponding to insertion event
- Throws:
ErrorMsg
- upon an error accessing data
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getInsertionQualities
java.lang.String getInsertionQualities() throws ErrorMsg
getInsertionQualities- Returns:
- qualities corresponding to insertion event
- Throws:
ErrorMsg
- upon an error accessing data
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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
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