Struct FiberFilters 

pub struct FiberFilters {
    pub bit_flag: Option<u16>,
    pub filter_expression: Option<String>,
    pub min_ml_score: u8,
    pub uncompressed: bool,
    pub strip_starting_basemods: i64,
    pub fire_filter: bool,
    pub skip_no_m6a: Option<bool>,
    pub min_msp: Option<usize>,
    pub min_ave_msp_size: Option<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: Option<u16>

BAM bit flags to filter on, equivalent to -F in samtools view Defaults to 0 (no filtering)

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

fire_filter: bool

Convenience: apply the FIRE peak-calling pipeline’s fiber-level filters (--skip-no-m6a, --min-msp 10, --min-ave-msp-size 10). Individual filter flags still override when both are set. Requires MSP/m6A annotations on the input BAM, so it is a no-op for commands that run before those annotations exist.

skip_no_m6a: Option<bool>

Drop fibers with no m6A calls. Off by default; --fire-filter turns this on unless explicitly set to false. Use --skip-no-m6a=false to override when --fire-filter is set.

min_msp: Option<usize>

Drop fibers with fewer than N MSP calls. Off (0) by default; --fire-filter sets this to 10 unless overridden.

min_ave_msp_size: Option<i64>

Drop fibers whose average MSP size is below N. Off (0) by default; --fire-filter sets this to 10 unless overridden.

Implementations

impl FiberFilters

pub fn get_bit_flag(&self) -> u16

Get the bit flag value, using a default if not explicitly set

pub fn resolved_skip_no_m6a(&self) -> bool

Resolved --skip-no-m6a, using --fire-filter as the fallback.

pub fn resolved_min_msp(&self) -> usize

Resolved --min-msp, using --fire-filter (10) as the fallback.

pub fn resolved_min_ave_msp_size(&self) -> i64

Resolved --min-ave-msp-size, using --fire-filter (10) as the fallback.

pub fn fire_filter_active(&self) -> bool

True if any FIRE fiber-level filter is active.

pub fn passes_fire_filter(&self, rec: &FiberseqData) -> bool

True if rec passes the FIRE fiber-level filters (skip_no_m6a, min_msp, min_ave_msp_size). Called by FiberseqRecords::next so every downstream consumer sees only filtered fibers.

Edge cases worth preserving:

• Fibers with zero MSPs are always rejected once any filter is active. The check also guards the divide-by-zero in the average MSP size below, so don’t drop it when refactoring.
• The no-m6a rejection is gated on resolved_skip_no_m6a() so --skip-no-m6a=false actually disables it (e.g. when combined with --fire-filter).

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.