Struct IdentifyArgs 

pub struct IdentifyArgs {
    pub input: PathBuf,
    pub input_format: Option<InputFormat>,
    pub max_matches: usize,
    pub exact_only: bool,
    pub catalog: Option<PathBuf>,
    pub hierarchical: bool,
    pub missing_contig_handling: MissingContigHandling,
    pub weight_match: u32,
    pub weight_coverage: u32,
    pub weight_order: u32,
    pub refget_server: Option<String>,
}

Fields

input: PathBuf

Input file (BAM, SAM, CRAM, FASTA, FAI, VCF, .dict, TSV, or CSV) Use ‘-’ for stdin (expects header text)

input_format: Option<InputFormat>

Input format (auto-detected by default)

max_matches: usize

Number of matches to show

exact_only: bool

Only show exact or near-exact matches

catalog: Option<PathBuf>

Path to custom catalog file

hierarchical: bool

Use hierarchical catalog format (required when –catalog points to a hierarchical catalog)

missing_contig_handling: MissingContigHandling

How to handle references with contigs missing from FASTA (e.g., CHM13 MT which uses standard rCRS mitochondria)

weight_match: u32

Weight for contig match score (0-100, default 70) How well query contigs match reference contigs

weight_coverage: u32

Weight for coverage score (0-100, default 20) What fraction of reference contigs are covered by query

weight_order: u32

Weight for order score (0-100, default 10) Whether contigs appear in the same order

refget_server: Option<String>

Refget server URL for looking up unknown contigs. When set, unmatched contigs with MD5 digests are queried against this server to retrieve aliases and other metadata.

Trait Implementations

impl Args for IdentifyArgs

fn group_id() -> Option<Id>

Report the ArgGroup::id for this set of arguments

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

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

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

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

impl FromArgMatches for IdentifyArgs

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

Assign values from ArgMatches to self.