public class AlignmentSpan
extends java.lang.Object
Modifier and Type | Field and Description |
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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 |
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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
|
int |
getCount() |
int |
getSpan() |
int |
getStart() |
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()