Package htsjdk.samtools.cram.structure
Class AlignmentSpan
- java.lang.Object
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- htsjdk.samtools.cram.structure.AlignmentSpan
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public class AlignmentSpan extends Object
A span of reads on a single reference.
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Field Summary
Fields Modifier and Type Field Description static AlignmentSpan
UNMAPPED_SPAN
A constant to represent an unmapped span.
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Constructor Summary
Constructors Constructor Description 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.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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 spanboolean
equals(Object obj)
int
getCount()
int
getSpan()
int
getStart()
int
hashCode()
void
setSpan(int span)
void
setStart(int start)
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Field Detail
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UNMAPPED_SPAN
public static final AlignmentSpan UNMAPPED_SPAN
A constant to represent an unmapped span.
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Constructor Detail
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AlignmentSpan
public AlignmentSpan(int start, int span)
Create a new span with a single read in it.- Parameters:
start
- alignment start of the spanspan
- alignment span
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AlignmentSpan
public AlignmentSpan(int start, int span, int count)
Create a new span with a multiple reads in it.- Parameters:
start
- alignment start of the spanspan
- alignment spancount
- number of reads in the span
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Method Detail
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add
public void add(int start, int span, int count)
Add multiple reads to the span.- Parameters:
start
- alignment startspan
- alignment spancount
- number of reads to add
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addSingle
public void addSingle(int start, int span)
Add a single read to the span- Parameters:
start
- alignment startspan
- read span on the reference
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getStart
public int getStart()
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setStart
public void setStart(int start)
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getSpan
public int getSpan()
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setSpan
public void setSpan(int span)
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getCount
public int getCount()
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