Struct QcOpts 

pub struct QcOpts {
    pub input: InputBam,
    pub out: String,
    pub acf: bool,
    pub acf_max_lag: usize,
    pub acf_min_m6a: usize,
    pub acf_max_reads: usize,
    pub acf_sample_rate: f32,
    pub m6a_per_msp: bool,
    pub n_reads: Option<usize>,
}

Fields

input: InputBam

out: String

Output text file with QC metrics. The format is a tab-separated file with the following columns: “statistic\tvalue\tcount” where “statistic” is the name of the metric, “value” is the value of the metric, and “count” is the number of times the metric was observed.

acf: bool

Calculate the auto-correlation function of the m6A marks in the fiber-seq data.

acf_max_lag: usize

maximum lag for the ACF calculation

acf_min_m6a: usize

Minimum number of m6A marks to use a read in the ACF calculation

acf_max_reads: usize

maximum number of reads to use in the ACF calculation

acf_sample_rate: f32

After sampling the first “acf-max-reads” randomly sample one of every “acf-sample-rate” reads and replace one of the previous reads at random.

m6a_per_msp: bool

In the output include a measure of the number of m6A events per MSPs of a given size. The output format is: “m6a_per_msp_size\t{m6A count},{MSP size},{is a FIRE}\t{count}” e.g. “m6a_per_msp_size\t35,100,false\t100”

n_reads: Option<usize>

Only process the first “n” reads in the input bam file.

Trait Implementations

impl Args for QcOpts

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 QcOpts

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

Formats the value using the given formatter.

impl FromArgMatches for QcOpts

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.