# Package picard.sam.util

package picard.sam.util

Related Packages
Package
Description
picard.sam
picard.sam.markduplicates
picard.sam.SamErrorMetric
Class
Description
Pair<X extends Comparable<X>, Y extends Comparable<Y>>
Simple Pair class.
PGTagArgumentCollection
Argument Collection which holds parameters common to classes that want to add PG tags to reads in SAM/BAM files
PhysicalLocation
Small interface that provides access to the physical location information about a cluster.
PhysicalLocationInt
Small class that provides access to the physical location information about a cluster.
PhysicalLocationShort
Small class that provides access to the physical location information about a cluster.
PrimaryAlignmentKey
It is useful to define a key such that the key will occur at most once among the primary alignments in a given file (assuming the file is valid).
ReadNameParser
Provides access to the physical location information about a cluster.
RepresentativeReadIndexer
Little struct-like class to hold a record index, the index of the corresponding representative read, and duplicate set size information.
SamComparison
Compare two SAM/BAM files.
SamComparison.AlignmentComparison
SAMComparisonArgumentCollection
Argument collection for SAM comparison