Struct PansnParameters 

pub struct PansnParameters {
    pub prefix: Option<String>,
    pub strip: bool,
    pub delimiter: char,
    pub hap1_tag: Option<String>,
    pub hap2_tag: Option<String>,
    pub min_mapq: u8,
    pub copy_header: Option<String>,
}

Fields

prefix: Option<String>

panSN-spec prefix to add to contig names (e.g., “HG002#1#”) If provided, adds the prefix. Mutually exclusive with –strip

strip: bool

Strip panSN-spec information from contig names Mutually exclusive with –prefix

delimiter: char

Delimiter character to use when stripping panSN-spec (default: ‘#’)

hap1_tag: Option<String>

Tag to identify haplotype 1 contigs (e.g., “haplotype1”) If both hap1-tag and hap2-tag are provided, reads will be tagged with HP based on contig names

hap2_tag: Option<String>

Tag to identify haplotype 2 contigs (e.g., “haplotype2”) If both hap1-tag and hap2-tag are provided, reads will be tagged with HP based on contig names

min_mapq: u8

The mapping quality must be greater than or equal to this value for haplotag assignment

copy_header: Option<String>

BAM file to copy header from (excluding SQ and HD tags)

Implementations

impl PansnParameters

pub fn has_operations(&self) -> bool

Check if any panSN operation is specified in the parameters

Trait Implementations

impl Args for PansnParameters

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 PansnParameters

fn clone(&self) -> PansnParameters

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for PansnParameters

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

Formats the value using the given formatter.

impl Default for PansnParameters

fn default() -> Self

Returns the “default value” for a type.

impl FromArgMatches for PansnParameters

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.