Uses of Class
org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser

Packages that use CmdLineParser

Package	Description
org.seqdoop.hadoop_bam.cli
org.seqdoop.hadoop_bam.cli.plugins
org.seqdoop.hadoop_bam.cli.plugins.chipster

Uses of CmdLineParser in org.seqdoop.hadoop_bam.cli

Methods in org.seqdoop.hadoop_bam.cli with parameters of type CmdLineParser

Modifier and Type	Method and Description
boolean	CLIMRPlugin.cacheAndSetProperties(CmdLineParser parser) Should be called before accessing any of the protected data such as verbose.
boolean	CLIMRBAMPlugin.cacheAndSetProperties(CmdLineParser parser) Should be called before accessing any of the protected data such as samFormat.
protected abstract int	CLIPlugin.run(CmdLineParser parser)

Uses of CmdLineParser in org.seqdoop.hadoop_bam.cli.plugins

Methods in org.seqdoop.hadoop_bam.cli.plugins with parameters of type CmdLineParser

Modifier and Type	Method and Description
protected int	Sort.run(CmdLineParser parser)
protected int	VCFSort.run(CmdLineParser parser)
protected int	FixMate.run(CmdLineParser parser)
protected int	View.run(CmdLineParser parser)
protected int	Index.run(CmdLineParser parser)
protected int	Cat.run(CmdLineParser parser)

Uses of CmdLineParser in org.seqdoop.hadoop_bam.cli.plugins.chipster

Methods in org.seqdoop.hadoop_bam.cli.plugins.chipster with parameters of type CmdLineParser

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