Struct InputModsBuilder 

pub struct InputModsBuilder<S: TagState + Args + FromArgMatches + Default> { /* private fields */ }

Builder for InputMods.

Implementations

impl<S: TagState + Args + FromArgMatches + Default + Clone> InputModsBuilder<S>

pub fn tag(&mut self, value: S) -> &mut Self

modified tag

pub fn mod_strand(&mut self, value: String) -> &mut Self

modified strand, set this to bc or bc_comp, meaning on basecalled strand or its complement. Some technologies like PacBio or ONT duplex can call mod data on both a strand and its complementary DNA and store it in the record corresponding to the strand, so you can use this filter to select only for mod data on a strand or its complement. Please note that this filter is different from selecting for forward or reverse aligned reads using the BAM flags.

pub fn mod_prob_filter(&mut self, value: ThresholdState) -> &mut Self

Filter to reject mods before analysis. Specify as low,high where both are fractions to reject modifications where the probabilities (p) are in this range e.g. “0.4,0.6” rejects 0.4 <= p <= 0.6. You can use this to reject ‘weak’ modification calls before analysis i.e. those with probabilities close to 0.5. NOTE: (1) Whether this filtration is applied or not, mods < 0.5 are considered unmodified and >= 0.5 are considered modified by our program. (2) mod probabilities are stored as a number from 0-255 in the modBAM format, so we internally convert 0.0-1.0 to 0-255. Default: reject nothing.

pub fn trim_read_ends_mod(&mut self, value: usize) -> &mut Self

Filter this many bp at the start and end of a read before any mod operations. Please note that the units here are bp and not units of base being queried.

pub fn base_qual_filter_mod(&mut self, value: u8) -> &mut Self

Exclude bases whose base quality is below this threshold before any mod operation, defaults to 0 i.e. unused. NOTE: (1) This step is only applied before modification operations, and not before any other operations. (2) No offsets such as +33 are needed here. (3) Modifications on reads where base quality information is not available are all rejected if this is non-zero.

pub fn mod_region(&mut self, value: String) -> &mut Self

Only keep modification data from this region

pub fn region_bed3(&mut self, value: Bed3<i32, u64>) -> &mut Self

Only keep modification data from this region. We do not expose this to the user, but infer it from the other options set by the user. We cannot populate this directly at the time of CLI parsing, as we need to look at the BAM header to convert a contig name into a numeric contig id.

pub fn build(&self) -> Result<InputMods<S>, Error>

Builds a new InputMods.

Errors

If a required field has not been initialized.

Trait Implementations

impl<S: Clone + TagState + Args + FromArgMatches + Default> Clone for InputModsBuilder<S>

fn clone(&self) -> InputModsBuilder<S>

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl<S: TagState + Args + FromArgMatches + Default + Clone> Default for InputModsBuilder<S>

fn default() -> Self

Returns the “default value” for a type.