Package htsjdk.samtools
Class AlignmentBlock
java.lang.Object
htsjdk.samtools.AlignmentBlock
- All Implemented Interfaces:
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:
-
Field Summary
-
Method Summary
Modifier and TypeMethodDescriptionint
The number of contiguous bases aligned to the reference.int
The first, 1-based, base in the read that is aligned to the reference reference.int
The first, 1-based, position in the reference to which the read is aligned.
-
Field Details
-
serialVersionUID
public static final long serialVersionUID- See Also:
-
-
Method Details
-
getReadStart
public int getReadStart()The first, 1-based, base in the read that is aligned to the reference reference. -
getReferenceStart
public int getReferenceStart()The first, 1-based, position in the reference to which the read is aligned. -
getLength
public int getLength()The number of contiguous bases aligned to the reference.
-