Struct CallPeaksOptions 

pub struct CallPeaksOptions {

    pub input: InputBam,
    pub shuffled: Option<String>,
    pub out: String,
    pub max_cov: Option<i32>,
    pub min_cov: Option<i32>,
    pub sd_cov: f64,
    pub max_fdr: f64,
    pub min_fire_frac: Option<f64>,
    pub min_fire_frac_filter: f64,
    pub min_frac_accessible: f64,
    pub window_size: usize,
    pub min_frac_overlap: f64,
    pub min_reciprocal_overlap: f64,
    pub high_reciprocal_overlap: f64,
    pub max_grouping_iterations: usize,
    pub fdr_table: Option<String>,
    pub fdr_table_out: Option<String>,
    pub include_nuc_msp: bool,
    pub haps: bool,
    pub min_fire_coverage: i32,
}

Fields

input: InputBam

shuffled: Option<String>

BED file with shuffled fiber positions (from bedtools shuffle) If not provided, will use all positions as real data (no FDR calculation)

out: String

Output BED file with called peaks

max_cov: Option<i32>

Maximum coverage threshold for filtering (optional)

min_cov: Option<i32>

Minimum coverage threshold for filtering (optional)

sd_cov: f64

Number of standard deviations from median coverage to use for filtering (default: 5) If set, will calculate median +/- (sd_cov * std_dev) and use those as min/max coverage This overrides –max-cov and –min-cov if those are not explicitly set

max_fdr: f64

Maximum FDR threshold for peak calling (ignored if –min-fire-frac is set)

min_fire_frac: Option<f64>

Minimum fraction of fibers with FIREs required to call a peak If set, skips FDR calculation and uses this threshold instead For example, 0.5 means at least 50% of fibers must have a FIRE at the peak position

min_fire_frac_filter: f64

Minimum fraction of fibers with FIREs required as an additional filter (applied WITH FDR) Unlike –min-fire-frac, this is applied in addition to FDR filtering, not instead of it For example, 0.3 means at least 30% of fibers must have a FIRE AND FDR must be <= max_fdr

min_frac_accessible: f64

Minimum fraction of accessible bases in peak

window_size: usize

Rolling window size for finding local maxima (in base pairs)

min_frac_overlap: f64

Minimum fraction of overlapping FIRE elements for merging peaks (Phase 2)

min_reciprocal_overlap: f64

Minimum reciprocal overlap for merging peaks (Phase 3)

high_reciprocal_overlap: f64

High reciprocal overlap threshold for initial merging (Phase 1)

max_grouping_iterations: usize

Maximum number of grouping iterations for merging

fdr_table: Option<String>

Skip the FDR table generation and use existing table

fdr_table_out: Option<String>

Output the FDR table to this file

include_nuc_msp: bool

Include nucleosome and MSP coverage in pileup (default: only FIRE coverage)

haps: bool

Include haplotype-specific calls

min_fire_coverage: i32

Minimum FIRE coverage required to calculate a score (default: 4)

Trait Implementations

impl Args for CallPeaksOptions

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 CallPeaksOptions

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

Formats the value using the given formatter.

impl FromArgMatches for CallPeaksOptions

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.