Enum Commands 

pub enum Commands {
    Init {
        title: Option<String>,
        description: Option<String>,
        registry: Option<String>,
        global: bool,
    },
    Register {
        label: String,
        fasta: Option<String>,
        genbank: Option<String>,
        gfa: Option<String>,
        gtf: Option<String>,
        gff: Option<String>,
        bed: Option<String>,
        tar: Option<String>,
        registry: Option<String>,
        global: bool,
    },
    Remove {
        label: String,
        registry: Option<String>,
        global: bool,
    },
    List {
        label: Option<String>,
        registry: Option<String>,
        global: bool,
    },
    Download {
        label: Option<String>,
        dest: Option<PathBuf>,
        registry: Option<String>,
        global: bool,
        all: bool,
    },
}

This enum encodes the CLI subcommands that refman exposes to users. Each variant represents a different operation that can be performed:

• Init: Creates a new reference registry without registering any datasets yet
• Register: Add a new dataset entry to the registry with an associated label
• Remove: Delete an existing dataset from the registry by its label
• List: Show all datasets currently in the registry
• Download: Fetch registered dataset files to the local filesystem

Each command takes various arguments to customize its behavior, like whether to use a global vs project-local registry, custom file paths, etc. Most commands require at minimum a dataset label to identify which reference data to operate on.

The registry itself is stored as a TOML file that tracks metadata about each registered dataset, including download URLs for supported file formats like FASTA, Genbank, GFF, etc.

Variants

Init

Fields

title: Option<String>

Optional project title

description: Option<String>

Optional project description

registry: Option<String>

Optional file path (absolute or relative) to the refman registry file.

global: bool

Whether to use a global registry as opposed to a project-specific registry

Register

Fields

label: String

Shorthand label for a dataset to register with refman. Once registered, this shorthand can be used to download and manage reference datasets in the future.

fasta: Option<String>

URL to simple reference sequence in FASTA format

genbank: Option<String>

URL to reference sequence, potentially with annotations, in Genbank format

gfa: Option<String>

URL to reference assemly in Graphical Fragment Assembly (GFA) format

gtf: Option<String>

URL to reference annotation data in Gene Transfer Format (GTF)

gff: Option<String>

URL to reference annotation data in General Feature Format (GFF3)

bed: Option<String>

URL to reference range data in Browser Extensible Data (BED) format

tar: Option<String>

URL to reference a TAR archive of arbitrary data

registry: Option<String>

Optional file path (absolute or relative) to the refman registry file.

global: bool

Whether to use a global registry as opposed to a project-specific registry

Remove

Fields

label: String

Shorthand label for a dataset to register with refman. Once registered, this shorthand can be used to download and manage reference datasets in the future.

registry: Option<String>

Optional file path (absolute or relative) to the refman registry file.

global: bool

Whether to use a global registry as opposed to a project-specific registry

List

Fields

label: Option<String>

Label string for a registered dataset

registry: Option<String>

Optional file path (absolute or relative) to the refman registry file.

global: bool

Whether to use a global registry as opposed to a project-specific registry

Download

Fields

label: Option<String>

Label string for a registered dataset

dest: Option<PathBuf>

Destination directory for downloaded files, defaulting to the current working directory.

registry: Option<String>

Optional file path (absolute or relative) to the refman registry file.

global: bool

Whether to use a global registry as opposed to a project-specific registry

all: bool

Whether to download all datasets in the registry

Trait Implementations

impl FromArgMatches for Commands

fn from_arg_matches(__clap_arg_matches: &ArgMatches) -> Result<Self, Error>

Instantiate Self from ArgMatches, parsing the arguments as needed.

fn from_arg_matches_mut( __clap_arg_matches: &mut ArgMatches, ) -> Result<Self, Error>

Instantiate Self from ArgMatches, parsing the arguments as needed.

fn update_from_arg_matches( &mut self, __clap_arg_matches: &ArgMatches, ) -> Result<(), Error>

Assign values from ArgMatches to self.

fn update_from_arg_matches_mut<'b>( &mut self, __clap_arg_matches: &mut ArgMatches, ) -> Result<(), Error>

Assign values from ArgMatches to self.

impl Subcommand for Commands

fn augment_subcommands<'b>(__clap_app: Command) -> Command

Append to Command so it can instantiate Self via FromArgMatches::from_arg_matches_mut

fn augment_subcommands_for_update<'b>(__clap_app: Command) -> Command

Append to Command so it can instantiate self via FromArgMatches::update_from_arg_matches_mut

fn has_subcommand(__clap_name: &str) -> bool

Test whether Self can parse a specific subcommand