Struct MockFireOptions 

pub struct MockFireOptions {
    pub bed: String,
    pub out: String,
    pub read_length: Option<i64>,
    pub quality: u8,
    pub uncompressed: bool,
    pub global: GlobalOpts,
}

Fields

bed: String

Input BED file where intervals become FIRE elements. Intervals are grouped into a mock read by chromosome and the 4th column (name), so a name reused across chromosomes yields one read per chromosome.

out: String

Output BAM file

read_length: Option<i64>

Length of mock reads (default: auto-calculated from BED intervals)

quality: u8

FIRE quality score to assign (0-255, higher = more confident FIRE call)

uncompressed: bool

Uncompressed BAM output (default: compressed)

global: GlobalOpts

Trait Implementations

impl Args for MockFireOptions

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 Debug for MockFireOptions

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

Formats the value using the given formatter.

impl FromArgMatches for MockFireOptions

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.