Struct fibertools_rs::cli::ExtractOptions

pub struct ExtractOptions {
    pub bam: String,
    pub reference: bool,
    pub molecular: bool,
    pub min_ml_score: u8,
    pub m6a: Option<String>,
    pub cpg: Option<String>,
    pub msp: Option<String>,
    pub nuc: Option<String>,
    pub all: Option<String>,
    pub quality: bool,
    pub simplify: bool,
}

Fields

bam: String

Input fiberseq bam file. If no path is provided extract will read bam data from stdin.

reference: bool

Report in reference sequence coordinates

molecular: bool

Report positions in the molecular sequence coordinates

min_ml_score: u8

Minium score in the ML tag to include in the output

m6a: Option<String>

Output path for m6a bed12

cpg: Option<String>

Output path for 5mC (CpG, primrose) bed12

msp: Option<String>

Output path for methylation sensitive patch (msp) bed12

nuc: Option<String>

Output path for nucleosome bed12

all: Option<String>

Output path for a tabular format including “all” fiberseq information in the bam

quality: bool

Include per base quality scores in “fiber_qual”

simplify: bool

Simplify output by remove fiber sequence

Trait Implementations

impl Args for ExtractOptions

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 ExtractOptions

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

Formats the value using the given formatter.

impl FromArgMatches for ExtractOptions

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 ExtractOptions

fn eq(&self, other: &ExtractOptions) -> 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 ExtractOptions

impl StructuralPartialEq for ExtractOptions