## Uses of Class
org.bdgenomics.cannoli.builder.CommandBuilder

### Uses of CommandBuilder in org.bdgenomics.cannoli.builder

Subclasses of CommandBuilder in org.bdgenomics.cannoli.builder
`class` `DockerBuilder` Docker container builder.
`class` `LocalBuilder` Local command builder.
`class` `SingularityBuilder` Singularity container builder.

Methods in org.bdgenomics.cannoli.builder that return CommandBuilder
`CommandBuilder` CommandBuilder.`add(Iterable<String> arguments)` Add one or more arguments to the list of command arguments for this command builder.
`CommandBuilder` CommandBuilder.`add(String... arguments)` Add one or more arguments to the list of command arguments for this command builder.
`CommandBuilder` CommandBuilder.`addArgument(String argument)` Add an argument to the list of command arguments for this command builder.
`CommandBuilder` CommandBuilder.`addArguments(Iterable<String> arguments)` Add one or more arguments to the list of command arguments for this command builder.
`CommandBuilder` CommandBuilder.`addArguments(String... arguments)` Add one or more arguments to the list of command arguments for this command builder.
`CommandBuilder` CommandBuilder.`addEnvironment(Map<String,String> environment)` Add environment variables to the map of environment variables for this command builder.
`CommandBuilder` CommandBuilder.`addEnvironment(String variable, String value)` Add an environment variable to the map of environment variables for this command builder.
`CommandBuilder` CommandBuilder.`addFile(String file)` Add a file to the list of files to make available locally for this command builder.
`CommandBuilder` CommandBuilder.`addFiles(Iterable<String> files)` Add files to the list of files to make available locally for this command builder.
`CommandBuilder` CommandBuilder.`addFiles(String... files)` Add zero or more files to the list of files to make available locally for this command builder.
`CommandBuilder` CommandBuilder.`addMount(String mount)` Add the specified mount point to the map of mount points for this command builder.
`CommandBuilder` CommandBuilder.`addMount(String source, String target)` Add the specified mount point to the map of mount points for this command builder.
`CommandBuilder` CommandBuilder.`addMounts(Map<String,String> mounts)` Add the specified mount points to the map of mount points for this command builder.
`static CommandBuilder` CommandBuilders.`create(boolean useDocker, boolean useSingularity)` Create a new Cannoli pipe command builder.
`CommandBuilder` CommandBuilder.`reset()` Reset this command builder.
`CommandBuilder` CommandBuilder.`setExecutable(String executable)` Set the executable for this command builder.
`CommandBuilder` CommandBuilder.`setFlankSize(Integer flankSize)` Set the number of bases to flank each command invocation by for this builder.
`CommandBuilder` CommandBuilder.`setImage(String image)` Set the image for this command builder.
`CommandBuilder` CommandBuilder.`setSudo(boolean sudo)` Set to true to run via sudo for this command builder.
`CommandBuilder` CommandBuilder.`setTimeout(Long timeout)` Set how long to let a single partition run for, in seconds, for this builder.
`CommandBuilder` CommandBuilder.`setTimeout(long duration, TimeUnit timeUnit)` Set how long to let a single partition run for, in the specified time unit, for this builder.