org.seqdoop.hadoop_bam.cli

Class CLIMRPlugin

java.lang.Object

org.apache.hadoop.conf.Configured

org.seqdoop.hadoop_bam.cli.CLIPlugin

org.seqdoop.hadoop_bam.cli.CLIMRPlugin

All Implemented Interfaces:

org.apache.hadoop.conf.Configurable

Direct Known Subclasses:

CLIMRBAMPlugin, Summarize, SummarySort, VCFSort

public abstract class CLIMRPlugin
extends CLIPlugin

Like CLIPlugin, but has lots of useful defaults for MapReduce-using plugins.

Field Summary

Fields

Modifier and Type	Field and Description
protected org.apache.hadoop.fs.Path	outPath
protected static CmdLineParser.Option	outputPathOpt
protected static CmdLineParser.Option	reducersOpt
protected int	reduceTasks
protected boolean	verbose
protected static CmdLineParser.Option	verboseOpt

Fields inherited from class org.seqdoop.hadoop_bam.cli.CLIPlugin

command, desc, longDesc, optionDescriptions, usageTail, version

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	CLIMRPlugin(String commandName, String description, String version, String usageParams, List<Pair<CmdLineParser.Option,String>> optionDescs, String longDescription)

Method Summary

Modifier and Type	Method and Description
boolean	cacheAndSetProperties(CmdLineParser parser) Should be called before accessing any of the protected data such as verbose.

Methods inherited from class org.seqdoop.hadoop_bam.cli.CLIPlugin

getCommandName, getDescription, main, printUsage, run

Methods inherited from class org.apache.hadoop.conf.Configured

getConf, setConf

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

verbose

protected boolean verbose

reduceTasks

protected int reduceTasks

outPath

protected org.apache.hadoop.fs.Path outPath

reducersOpt

protected static final CmdLineParser.Option reducersOpt

verboseOpt

protected static final CmdLineParser.Option verboseOpt

outputPathOpt

protected static final CmdLineParser.Option outputPathOpt

Constructor Detail

CLIMRPlugin

protected CLIMRPlugin(String commandName,
                      String description,
                      String version,
                      String usageParams,
                      List<Pair<CmdLineParser.Option,String>> optionDescs,
                      String longDescription)

Method Detail

cacheAndSetProperties

public boolean cacheAndSetProperties(CmdLineParser parser)

Should be called before accessing any of the protected data such as verbose.