Struct fibertools_rs::cli::CenterOptions

pub struct CenterOptions {
    pub bam: String,
    pub bed: String,
    pub min_ml_score: u8,
    pub dist: Option<i64>,
    pub wide: bool,
    pub reference: bool,
    pub simplify: bool,
}

Fields

bam: String

Aligned Fiber-seq bam file.

bed: String

Bed file on which to center fiberseq reads. Data is adjusted to the start position of the bed file and corrected for strand if the strand is indicated in the 6th column of the bed file. The 4th column will also be checked for the strand but only after the 6th is.
If you include strand information in the 4th (or 6th) column it will orient data accordingly and use the end position of bed record instead of the start if on the minus strand. This means that profiles of motifs in both the forward and minus orientation will align to the same central position.

min_ml_score: u8

Minium score in the ML tag to include in the output

dist: Option<i64>

Set a maximum distance from the start of the motif to keep a feature

wide: bool

Provide data in wide format, one row per read

reference: bool

Return relative reference position instead of relative molecular position

simplify: bool

Replace the sequence output column with just “N”.

Trait Implementations

impl Args for CenterOptions

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.

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

Append to Command so it can update self.

impl Debug for CenterOptions

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

Formats the value using the given formatter.

impl FromArgMatches for CenterOptions

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 PartialEq for CenterOptions

fn eq(&self, other: &CenterOptions) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl Eq for CenterOptions

impl StructuralPartialEq for CenterOptions