htsjdk.samtools.cram.encoding.readfeatures (htsjdk 2.24.1 API)

Interface Summary
Interface Description

ReadFeature
An interface to capture data in read coordinates.

Interface Summary
Interface	Description
ReadFeature	An interface to capture data in read coordinates.

Class Summary
Class	Description
BaseQualityScore	A read feature representing a single quality score in a read.
Bases
Deletion	A read feature representing a deletion of one or more bases similar to `CigarOperator.D`.
HardClip	A read feature representing a hard clip similar to `CigarOperator.H`.
InsertBase	A read feature representing a single insert base.
Insertion	A read feature representing a multi-base insertion.
Padding	A read feature representing padding, similar to `CigarOperator.P`.
ReadBase	A read feature representing a single base with associated quality score.
RefSkip	A read feature representing a reference skip similar to `CigarOperator.N`.
Scores	A read feature representing a contiguous stretch of quality scores in a read.
SoftClip	A read feature representing a soft clip similar to `CigarOperator.S`.
Substitution	A substitution event captured in read coordinates.

Package htsjdk.samtools.cram.encoding.readfeatures