org.seqdoop.hadoop_bam.cli

Class CLIMRBAMPlugin

java.lang.Object

org.apache.hadoop.conf.Configured

org.seqdoop.hadoop_bam.cli.CLIPlugin

org.seqdoop.hadoop_bam.cli.CLIMRPlugin

org.seqdoop.hadoop_bam.cli.CLIMRBAMPlugin

All Implemented Interfaces:

org.apache.hadoop.conf.Configurable

Direct Known Subclasses:

FixMate, Sort

public abstract class CLIMRBAMPlugin
extends CLIMRPlugin

Like CLIMRPlugin, with added useful defaults for plugins working solely on BAM/SAM files. Adds an option description for the "-o" option in CLIMRPlugin, so subclasses shouldn't.

Field Summary

Fields

Modifier and Type	Field and Description
protected static CmdLineParser.Option	formatOpt
protected static CmdLineParser.Option	noTrustExtsOpt
protected SAMFormat	samFormat

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

outPath, outputPathOpt, reducersOpt, reduceTasks, verbose, 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	CLIMRBAMPlugin(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 samFormat.

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

samFormat

protected SAMFormat samFormat

formatOpt

protected static final CmdLineParser.Option formatOpt

noTrustExtsOpt

protected static final CmdLineParser.Option noTrustExtsOpt

Constructor Detail

CLIMRBAMPlugin

protected CLIMRBAMPlugin(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 samFormat.

Overrides:

cacheAndSetProperties in class CLIMRPlugin