Struct IndexOptions 

pub struct IndexOptions {
    pub blobdir: Option<PathBuf>,
    pub window_size: Vec<f64>,
    pub taxon_id: Option<String>,
    pub datasets_accession: Option<String>,
    pub busco: Option<Vec<PathBuf>>,
    pub schema: bool,
    pub out: Option<PathBuf>,
}

Options to pass to blobtk index

Fields

blobdir: Option<PathBuf>

Path to BlobDir directory containing files to index

window_size: Vec<f64>

Window sizes for feature extraction. Supported values depend on the BlobDir (typically 0.01, 0.1, 1, 100000, 1000000)

taxon_id: Option<String>

Taxon ID for the assembly

datasets_accession: Option<String>

Assembly accession to fetch sequence report from NCBI datasets

busco: Option<Vec<PathBuf>>

Path to BUSCO directory containing files to index Multiple BUSCO directories can be provided

schema: bool

Flag to generate JSON schema

out: Option<PathBuf>

Output schema file name

Trait Implementations

impl Args for IndexOptions

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 CommandFactory for IndexOptions

fn command<'b>() -> Command

Build a Command that can instantiate Self.

fn command_for_update<'b>() -> Command

Build a Command that can update self.

impl Debug for IndexOptions

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl FromArgMatches for IndexOptions

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.

impl Parser for IndexOptions

fn parse() -> Self

Parse from std::env::args_os(), exit on error.

fn try_parse() -> Result<Self, Error>

Parse from std::env::args_os(), return Err on error.

fn parse_from<I, T>(itr: I) -> Self

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Parse from iterator, exit on error.

fn try_parse_from<I, T>(itr: I) -> Result<Self, Error>

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Parse from iterator, return Err on error.

fn update_from<I, T>(&mut self, itr: I)

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Update from iterator, exit on error.

fn try_update_from<I, T>(&mut self, itr: I) -> Result<(), Error>

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Update from iterator, return Err on error.