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