A B C D F G I L O R S

## A

add(String...) - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Add one or more arguments to the list of command arguments for this command builder.
add(Iterable<String>) - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Add one or more arguments to the list of command arguments for this command builder.
addArgument(String) - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Add an argument to the list of command arguments for this command builder.
addArguments(String...) - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Add one or more arguments to the list of command arguments for this command builder.
addArguments(Iterable<String>) - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Add one or more arguments to the list of command arguments for this command builder.
addEnvironment(String, String) - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Add an environment variable to the map of environment variables for this command builder.
addEnvironment(Map<String, String>) - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Add environment variables to the map of environment variables for this command builder.
addFile(String) - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Add a file to the list of files to make available locally for this command builder.
addFiles(String...) - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Add zero or more files to the list of files to make available locally for this command builder.
addFiles(Iterable<String>) - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Add files to the list of files to make available locally for this command builder.
addMount(String) - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Add the specified mount point to the map of mount points for this command builder.
addMount(String, String) - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Add the specified mount point to the map of mount points for this command builder.
addMounts(Map<String, String>) - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Add the specified mount points to the map of mount points for this command builder.

## B

build() - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Build and return the command for this command builder as a list of strings.
build() - Method in class org.bdgenomics.cannoli.builder.LocalBuilder

## C

CommandBuilder - Class in org.bdgenomics.cannoli.builder
  Abstract command builder.
CommandBuilder() - Constructor for class org.bdgenomics.cannoli.builder.CommandBuilder
  Create a new command builder.
CommandBuilder(String) - Constructor for class org.bdgenomics.cannoli.builder.CommandBuilder
  Create a new command builder with the specified executable.
CommandBuilders - Class in org.bdgenomics.cannoli.builder
  Cannoli pipe command builders.
CommandBuilders() - Constructor for class org.bdgenomics.cannoli.builder.CommandBuilders
create(boolean, boolean) - Static method in class org.bdgenomics.cannoli.builder.CommandBuilders
  Create a new Cannoli pipe command builder.

## D

DockerBuilder - Class in org.bdgenomics.cannoli.builder
  Docker container builder.
DockerBuilder() - Constructor for class org.bdgenomics.cannoli.builder.DockerBuilder
  Create a new Docker command builder.
DockerBuilder(String) - Constructor for class org.bdgenomics.cannoli.builder.DockerBuilder
  Create a new Docker command builder with the specified executable.
DockerBuilder(String, String) - Constructor for class org.bdgenomics.cannoli.builder.DockerBuilder
  Create a new Docker command builder with the specified executable and image.

## F

formatEnvironmentArgument(String, String) - Method in class org.bdgenomics.cannoli.builder.DockerBuilder
formatEnvironmentArgument(String, String) - Method in class org.bdgenomics.cannoli.builder.SingularityBuilder
formatEnvironmentVariable(String, String) - Method in class org.bdgenomics.cannoli.builder.DockerBuilder
formatEnvironmentVariable(String, String) - Method in class org.bdgenomics.cannoli.builder.SingularityBuilder
formatImage(String) - Method in class org.bdgenomics.cannoli.builder.DockerBuilder
formatImage(String) - Method in class org.bdgenomics.cannoli.builder.SingularityBuilder
formatMount(String, String) - Method in class org.bdgenomics.cannoli.builder.DockerBuilder
formatMount(String, String) - Method in class org.bdgenomics.cannoli.builder.SingularityBuilder

## G

getArguments() - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Return an immutable list of command arguments for this command builder.
getContainerCommands() - Method in class org.bdgenomics.cannoli.builder.DockerBuilder
getContainerCommands() - Method in class org.bdgenomics.cannoli.builder.SingularityBuilder
getEnvironment() - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Return an immutable map of environment variables for this command builder.
getExecutable() - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Return the executable for this command builder.
getFiles() - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Return an immutable list of files to make available locally for this command builder.
getFlankSize() - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Return the number of bases to flank each command invocation by for this builder.
getImage() - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Return the image for this command builder.
getMounts() - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Return the map of mount points for this command builder.
getOptFlankSize() - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Return the number of bases to flank each command invocation by for this builder, as an optional.
getOptTimeout() - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Return how long to let a single partition run for, in seconds, for this builder, as an optional.
getRemoveArgument() - Method in class org.bdgenomics.cannoli.builder.DockerBuilder
getRemoveArgument() - Method in class org.bdgenomics.cannoli.builder.SingularityBuilder
getSudo() - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Return true to run via sudo for this command builder.
getTimeout() - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Return how long to let a single partition run for, in seconds, for this builder.

## I

isSudo() - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Return true to run via sudo for this command builder.

## L

LocalBuilder - Class in org.bdgenomics.cannoli.builder
  Local command builder.
LocalBuilder() - Constructor for class org.bdgenomics.cannoli.builder.LocalBuilder
  Create a new local command builder.
LocalBuilder(String) - Constructor for class org.bdgenomics.cannoli.builder.LocalBuilder
  Create a new local command builder with the specified executable.

## O

org.bdgenomics.cannoli.builder - package org.bdgenomics.cannoli.builder
  Cannoli pipe command builder.

## R

reset() - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Reset this command builder.

## S

setExecutable(String) - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Set the executable for this command builder.
setFlankSize(Integer) - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Set the number of bases to flank each command invocation by for this builder.
setImage(String) - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Set the image for this command builder.
setSudo(boolean) - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Set to true to run via sudo for this command builder.
setTimeout(Long) - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Set how long to let a single partition run for, in seconds, for this builder.
setTimeout(long, TimeUnit) - Method in class org.bdgenomics.cannoli.builder.CommandBuilder
  Set how long to let a single partition run for, in the specified time unit, for this builder.
SingularityBuilder - Class in org.bdgenomics.cannoli.builder
  Singularity container builder.
SingularityBuilder() - Constructor for class org.bdgenomics.cannoli.builder.SingularityBuilder
  Create a new Singularity command builder.
SingularityBuilder(String) - Constructor for class org.bdgenomics.cannoli.builder.SingularityBuilder
  Create a new Singularity command builder with the specified executable.
SingularityBuilder(String, String) - Constructor for class org.bdgenomics.cannoli.builder.SingularityBuilder
  Create a new Singularity command builder with the specified executable and image.

A B C D F G I L O R S