Enum CatalogCommands 

pub enum CatalogCommands {
    List {
        catalog: Option<PathBuf>,
        assembly: Option<String>,
        source: Option<String>,
    },
    Show {
        id: String,
        catalog: Option<PathBuf>,
        all_contigs: bool,
    },
    Export {
        output: PathBuf,
        catalog: Option<PathBuf>,
    },
    ListHierarchical {
        catalog: PathBuf,
    },
    BuildHierarchical {

        id: String,
        name: String,
        inputs: Vec<PathBuf>,
        assembly_id: Option<String>,
        version_id: Option<String>,
        source: Option<String>,
        download_url: Option<String>,
        tags: Option<String>,
        output: Option<PathBuf>,
        append_to: Option<PathBuf>,
        force: bool,
        require_md5: bool,
        infer_assembly: Option<Option<PathBuf>>,
        no_generate_ucsc_names: bool,
    
},
    Build {

        id: String,
        name: String,
        inputs: Vec<PathBuf>,
        assembly: Option<String>,
        source: Option<String>,
        description: Option<String>,
        download_url: Option<String>,
        assembly_report_url: Option<String>,
        tags: Option<String>,
        output: Option<PathBuf>,
        append_to: Option<PathBuf>,
        force: bool,
        input_format: Option<InputFormatArg>,
        require_md5: bool,
        no_generate_ucsc_names: bool,
    
},
}

Variants

List

List all references in the catalog

Fields

catalog: Option<PathBuf>

Path to custom catalog file

assembly: Option<String>

Filter by assembly (e.g., “GRCh38”)

source: Option<String>

Filter by source (e.g., “UCSC”)

Show

Show details of a specific reference

Fields

id: String

Reference ID

catalog: Option<PathBuf>

Path to custom catalog file

all_contigs: bool

Show all contigs

Export

Export the catalog to a file

Fields

output: PathBuf

Output file path

catalog: Option<PathBuf>

Path to custom catalog file to export (defaults to embedded)

ListHierarchical

List hierarchical catalog contents (assemblies, versions, distributions)

Fields

catalog: PathBuf

Path to hierarchical catalog file

BuildHierarchical

Build a hierarchical catalog entry (FastaDistribution)

Fields

id: String

Distribution ID (e.g., “hg38_custom”)

name: String

Display name (e.g., “hg38 Custom Build”)

inputs: Vec<PathBuf>

Input file(s) - can be specified multiple times

assembly_id: Option<String>

Assembly ID to attach to (e.g., “grch38”)

version_id: Option<String>

Version ID to attach to (e.g., “grch38_p14”)

source: Option<String>

Source organization (ucsc, ncbi, broad, ensembl, 1kg, dragen, gdc, or custom)

download_url: Option<String>

Reference FASTA download URL

tags: Option<String>

Tags (comma-separated)

output: Option<PathBuf>

Output file (creates new hierarchical catalog or standalone distribution JSON)

append_to: Option<PathBuf>

Append to existing hierarchical catalog

force: bool

Overwrite if distribution ID already exists

require_md5: bool

Require MD5 checksums for all contigs

infer_assembly: Option<Option<PathBuf>>

Infer base assembly by matching MD5s against an existing catalog If no path given, uses the embedded catalog (or –append-to catalog)

no_generate_ucsc_names: bool

Disable automatic generation of UCSC-style names for patches.

By default, when parsing NCBI assembly reports, UCSC-style names are generated for fix-patches and novel-patches that have “na” in the UCSC-style-name column (common in reports prior to p13).

Use this flag to disable this behavior and only use names explicitly present in the assembly report.

See: https://genome.ucsc.edu/FAQ/FAQdownloads.html

Build

Build a new reference entry from input files

Fields

id: String

Unique reference ID (e.g., “grch38_custom”)

name: String

Display name (e.g., “GRCh38 Custom Build”)

inputs: Vec<PathBuf>

Input file(s) - can be specified multiple times Supported formats: .dict, .fai, .sam, .bam, .cram, .vcf, _assembly_report.txt

assembly: Option<String>

Assembly version (grch37, grch38, or custom name)

source: Option<String>

Source organization (ucsc, ncbi, broad, ensembl, illumina, 1kg, or custom)

description: Option<String>

Description text

download_url: Option<String>

Reference FASTA download URL

assembly_report_url: Option<String>

NCBI assembly report URL

tags: Option<String>

Comma-separated tags

output: Option<PathBuf>

Output file (JSON). If not specified, prints to stdout

append_to: Option<PathBuf>

Append to existing catalog file

force: bool

Force overwrite if ID already exists in catalog

input_format: Option<InputFormatArg>

Force input format instead of auto-detection

require_md5: bool

Error if any contig lacks MD5 checksum

no_generate_ucsc_names: bool

Disable automatic generation of UCSC-style names for patches.

By default, when parsing NCBI assembly reports, UCSC-style names are generated for fix-patches and novel-patches that have “na” in the UCSC-style-name column (common in reports prior to p13).

Use this flag to disable this behavior and only use names explicitly present in the assembly report.

See: https://genome.ucsc.edu/FAQ/FAQdownloads.html

Trait Implementations

impl FromArgMatches for CatalogCommands

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 CatalogCommands

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