org.seqdoop.hadoop_bam.cli.plugins

Class FixMate

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

org.seqdoop.hadoop_bam.cli.plugins.FixMate

All Implemented Interfaces:

org.apache.hadoop.conf.Configurable

public final class FixMate
extends CLIMRBAMPlugin

Field Summary

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

formatOpt, noTrustExtsOpt, 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

Constructor and Description
FixMate()

Method Summary

Modifier and Type	Method and Description
protected int	run(CmdLineParser parser)

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

cacheAndSetProperties

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

getCommandName, getDescription, main, printUsage

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

Constructor Detail

FixMate

public FixMate()

Method Detail

run

protected int run(CmdLineParser parser)

Specified by:

run in class CLIPlugin