Uses of Package
org.snpeff.snpEffect.commandLine
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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 Note: This is done in order to see potential incompatibility errors between genome sequence and annotation.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.snpEffect.commandLine.eff Class Description SnpEffCmdEff Command line program: Predict variant effects -
Classes in org.snpeff.snpEffect.commandLine used by org.snpeff.snpEffect.testCases.integration 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.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(); }