# Uses of Package
org.snpeff.snpEffect.commandLine

Packages that use org.snpeff.snpEffect.commandLine
Package
Description
org.snpeff
org.snpeff.fastq
org.snpeff.snpEffect
org.snpeff.snpEffect.commandLine
org.snpeff.spliceSites

Classes in org.snpeff.snpEffect.commandLine used by org.snpeff
Class
Description
CommandLine
Command line and arguments The way to run a command from 'main' is usually: public static void main(String[] args) { Command cmd = new Command(); cmd.parseArgs(args); cmd.run(); }
Classes in org.snpeff.snpEffect.commandLine used by org.snpeff.fastq
Class
Description
CommandLine
Command line and arguments The way to run a command from 'main' is usually: public static void main(String[] args) { Command cmd = new Command(); cmd.parseArgs(args); cmd.run(); }
Classes in org.snpeff.snpEffect.commandLine used by org.snpeff.snpEffect
Class
Description
CommandLine
Command line and arguments The way to run a command from 'main' is usually: public static void main(String[] args) { Command cmd = new Command(); cmd.parseArgs(args); cmd.run(); }
Classes in org.snpeff.snpEffect.commandLine used by org.snpeff.snpEffect.commandLine
Class
Description
CommandLine
Command line and arguments The way to run a command from 'main' is usually: public static void main(String[] args) { Command cmd = new Command(); cmd.parseArgs(args); cmd.run(); }
SnpEffCmdCds
Command line: Calculate coding sequences from a file and compare them to the ones calculated from our data structures
SnpEffCmdDump.DumpFormat
SnpEffCmdProtein
Command line: Read protein sequences from a file and compare them to the ones calculated from our data structures Note: This is done in order to see potential incompatibility errors between genome sequence and annotation.
Classes in org.snpeff.snpEffect.commandLine used by org.snpeff.spliceSites
Class
Description
CommandLine
Command line and arguments The way to run a command from 'main' is usually: public static void main(String[] args) { Command cmd = new Command(); cmd.parseArgs(args); cmd.run(); }