# Package htsjdk.samtools.cram.encoding.readfeatures

package htsjdk.samtools.cram.encoding.readfeatures

Related Packages
Package
Description
htsjdk.samtools.cram.encoding
htsjdk.samtools.cram.encoding.core
htsjdk.samtools.cram.encoding.external
htsjdk.samtools.cram.encoding.reader
htsjdk.samtools.cram.encoding.writer
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.
ReadFeature
An interface to capture data in read coordinates.
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.