Struct FiberFilters

pub struct FiberFilters {
    pub bit_flag: u16,
    pub filter_expression: Option<String>,
    pub min_ml_score: u8,
    pub uncompressed: bool,
    pub strip_starting_basemods: i64,
}

This struct establishes the way a Fiber-seq bam should be filtered when it is read in. This struct is both used as an argument for building FiberSeq records and as a struct that is parsed into cli arguments.

Fields

bit_flag: u16

BAM bit flags to filter on, equivalent to -F in samtools view

filter_expression: Option<String>

Filtering expression to use for filtering records Example: filter to nucleosomes with lengths greater than 150 bp -x “len(nuc)>150” Example: filter to msps with lengths between 30 and 49 bp -x “len(msp)=30:50” Example: combine 2+ filter expressions -x “len(nuc)<150,len(msp)=30:50” Filtering expressions support len() and qual() functions over msp, nuc, m6a, cpg

min_ml_score: u8

Minium score in the ML tag to use or include in the output

uncompressed: bool

Output uncompressed BAM files

strip_starting_basemods: i64

strip basemods in the first or last X bp of the read

Implementations

impl FiberFilters

pub fn filter_on_bit_flags<'a, I>( &'a self, records: I, ) -> impl Iterator<Item = Record> + 'a

where I: IntoIterator<Item = Result<Record, Error>> + 'a,

This function accepts an iterator over bam records and filters them based on the bit flag.

Trait Implementations

impl Args for FiberFilters

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 Clone for FiberFilters

fn clone(&self) -> FiberFilters

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for FiberFilters

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

Formats the value using the given formatter.

impl Default for FiberFilters

fn default() -> Self

Returns the “default value” for a type.

impl FromArgMatches for FiberFilters

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.