Uses of Package
picard.cmdline

Packages that use picard.cmdline

Package	Description
picard.analysis
picard.analysis.artifacts
picard.analysis.directed
picard.analysis.replicates
picard.cmdline
picard.cmdline.programgroups
picard.fastq
picard.fingerprint
picard.illumina
picard.illumina.quality
picard.reference
picard.sam
picard.sam.markduplicates
picard.sam.markduplicates.util
picard.util
picard.vcf
picard.vcf.filter

Classes in picard.cmdline used by picard.analysis

Class and Description
CommandLineProgram Abstract class to facilitate writing command-line programs.
CommandLineProgramProperties Annotates a command line program with various properties, such as usage (short and long), as well as to which program group it belongs.
Option Used to annotate which fields of a CommandLineProgram are options given at the command line.
PositionalArguments Used to annotate which field of a CommandLineProgram should store parameters given at the command line which are not options.

Classes in picard.cmdline used by picard.analysis.artifacts

Class and Description
CommandLineProgram Abstract class to facilitate writing command-line programs.
CommandLineProgramProperties Annotates a command line program with various properties, such as usage (short and long), as well as to which program group it belongs.
Option Used to annotate which fields of a CommandLineProgram are options given at the command line.

Classes in picard.cmdline used by picard.analysis.directed

Class and Description
CommandLineProgram Abstract class to facilitate writing command-line programs.
CommandLineProgramProperties Annotates a command line program with various properties, such as usage (short and long), as well as to which program group it belongs.
Option Used to annotate which fields of a CommandLineProgram are options given at the command line.

Classes in picard.cmdline used by picard.analysis.replicates

Class and Description
CommandLineProgram Abstract class to facilitate writing command-line programs.
CommandLineProgramProperties Annotates a command line program with various properties, such as usage (short and long), as well as to which program group it belongs.
Option Used to annotate which fields of a CommandLineProgram are options given at the command line.

Classes in picard.cmdline used by picard.cmdline

Class and Description
CommandLineParser Annotation-driven utility for parsing command-line arguments, checking for errors, and producing usage message.
CommandLineParser.OptionDefinition
CommandLineProgramGroup Interface for groups of CommandLinePrograms.
CommandLineProgramProperties Annotates a command line program with various properties, such as usage (short and long), as well as to which program group it belongs.
Option Used to annotate which fields of a CommandLineProgram are options given at the command line.

Classes in picard.cmdline used by picard.cmdline.programgroups

Class and Description
CommandLineProgramGroup Interface for groups of CommandLinePrograms.

Classes in picard.cmdline used by picard.fastq

Class and Description
CommandLineProgram Abstract class to facilitate writing command-line programs.
CommandLineProgramProperties Annotates a command line program with various properties, such as usage (short and long), as well as to which program group it belongs.
Option Used to annotate which fields of a CommandLineProgram are options given at the command line.

Classes in picard.cmdline used by picard.fingerprint

Class and Description
CommandLineProgram Abstract class to facilitate writing command-line programs.
CommandLineProgramProperties Annotates a command line program with various properties, such as usage (short and long), as well as to which program group it belongs.
Option Used to annotate which fields of a CommandLineProgram are options given at the command line.

Classes in picard.cmdline used by picard.illumina

Class and Description
CommandLineProgram Abstract class to facilitate writing command-line programs.
CommandLineProgramProperties Annotates a command line program with various properties, such as usage (short and long), as well as to which program group it belongs.
Option Used to annotate which fields of a CommandLineProgram are options given at the command line.

Classes in picard.cmdline used by picard.illumina.quality

Class and Description
CommandLineProgram Abstract class to facilitate writing command-line programs.
CommandLineProgramProperties Annotates a command line program with various properties, such as usage (short and long), as well as to which program group it belongs.
Option Used to annotate which fields of a CommandLineProgram are options given at the command line.

Classes in picard.cmdline used by picard.reference

Class and Description
CommandLineProgram Abstract class to facilitate writing command-line programs.
CommandLineProgramProperties Annotates a command line program with various properties, such as usage (short and long), as well as to which program group it belongs.
Option Used to annotate which fields of a CommandLineProgram are options given at the command line.

Classes in picard.cmdline used by picard.sam

Class and Description
CommandLineProgram Abstract class to facilitate writing command-line programs.
CommandLineProgramProperties Annotates a command line program with various properties, such as usage (short and long), as well as to which program group it belongs.
Option Used to annotate which fields of a CommandLineProgram are options given at the command line.
PositionalArguments Used to annotate which field of a CommandLineProgram should store parameters given at the command line which are not options.

Classes in picard.cmdline used by picard.sam.markduplicates

Class and Description
CommandLineProgram Abstract class to facilitate writing command-line programs.
CommandLineProgramProperties Annotates a command line program with various properties, such as usage (short and long), as well as to which program group it belongs.
Option Used to annotate which fields of a CommandLineProgram are options given at the command line.

Classes in picard.cmdline used by picard.sam.markduplicates.util

Class and Description
CommandLineProgram Abstract class to facilitate writing command-line programs.
Option Used to annotate which fields of a CommandLineProgram are options given at the command line.

Classes in picard.cmdline used by picard.util

Class and Description
CommandLineParser.ClpEnum
CommandLineProgram Abstract class to facilitate writing command-line programs.
CommandLineProgramProperties Annotates a command line program with various properties, such as usage (short and long), as well as to which program group it belongs.
Option Used to annotate which fields of a CommandLineProgram are options given at the command line.

Classes in picard.cmdline used by picard.vcf

Class and Description
CommandLineProgram Abstract class to facilitate writing command-line programs.
CommandLineProgramProperties Annotates a command line program with various properties, such as usage (short and long), as well as to which program group it belongs.
Option Used to annotate which fields of a CommandLineProgram are options given at the command line.

Classes in picard.cmdline used by picard.vcf.filter

Class and Description
CommandLineProgram Abstract class to facilitate writing command-line programs.
CommandLineProgramProperties Annotates a command line program with various properties, such as usage (short and long), as well as to which program group it belongs.
Option Used to annotate which fields of a CommandLineProgram are options given at the command line.