public class AlignmentSpan
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static AlignmentSpan |
UNMAPPED_SPAN
A constant to represent an unmapped span.
|
Constructor and Description |
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AlignmentSpan(int start,
int span)
Create a new span with a single read in it.
|
AlignmentSpan(int start,
int span,
int count)
Create a new span with a multiple reads in it.
|
Modifier and Type | Method and Description |
---|---|
void |
add(int start,
int span,
int count)
Add multiple reads to the span.
|
void |
addSingle(int start,
int span)
Add a single read to the span
|
boolean |
equals(java.lang.Object obj) |
int |
getCount() |
int |
getSpan() |
int |
getStart() |
int |
hashCode() |
void |
setSpan(int span) |
void |
setStart(int start) |
public static final AlignmentSpan UNMAPPED_SPAN
public AlignmentSpan(int start, int span)
start
- alignment start of the spanspan
- alignment spanpublic AlignmentSpan(int start, int span, int count)
start
- alignment start of the spanspan
- alignment spancount
- number of reads in the spanpublic void add(int start, int span, int count)
start
- alignment startspan
- alignment spancount
- number of reads to addpublic void addSingle(int start, int span)
start
- alignment startspan
- read span on the referencepublic int getStart()
public void setStart(int start)
public int getSpan()
public void setSpan(int span)
public int getCount()
public boolean equals(java.lang.Object obj)
equals
in class java.lang.Object
public int hashCode()
hashCode
in class java.lang.Object