Package htsjdk.samtools
Class AlignmentBlock
- java.lang.Object
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- htsjdk.samtools.AlignmentBlock
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- All Implemented Interfaces:
Serializable
public class AlignmentBlock extends Object implements Serializable
Represents the contiguous alignment of a subset of read bases to a reference sequence. Simply put an alignment block tells you that read bases from readStart are aligned to the reference (matching or mismatching) from referenceStart for length bases.- See Also:
- Serialized Form
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Field Summary
Fields Modifier and Type Field Description static long
serialVersionUID
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
getLength()
The number of contiguous bases aligned to the reference.int
getReadStart()
The first, 1-based, base in the read that is aligned to the reference reference.int
getReferenceStart()
The first, 1-based, position in the reference to which the read is aligned.
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Field Detail
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serialVersionUID
public static final long serialVersionUID
- See Also:
- Constant Field Values
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Method Detail
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getReadStart
public int getReadStart()
The first, 1-based, base in the read that is aligned to the reference reference.
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getReferenceStart
public int getReferenceStart()
The first, 1-based, position in the reference to which the read is aligned.
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getLength
public int getLength()
The number of contiguous bases aligned to the reference.
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