Struct ScoreArgs 

pub struct ScoreArgs {
    pub query: PathBuf,
    pub reference: PathBuf,
    pub symmetric: bool,
    pub weight_match: u32,
    pub weight_coverage: u32,
    pub weight_order: u32,
}

Arguments for the score command

Fields

query: PathBuf

Query file (the file you want to score) Supports: BAM, SAM, CRAM, FASTA, FAI, VCF, .dict, TSV, CSV

reference: PathBuf

Reference file (the file to compare against) Supports: BAM, SAM, CRAM, FASTA, FAI, VCF, .dict, TSV, CSV

symmetric: bool

Also compute the reverse comparison (reference as query, query as reference). By default, scoring is asymmetric: it measures how well the query matches the reference. With –symmetric, both directions are computed.

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

Trait Implementations

impl Args for ScoreArgs

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 ScoreArgs

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.