Struct PgLiftOptions 

pub struct PgLiftOptions {

    pub reference: String,
    pub input: String,
    pub bam: bool,
    pub graph: String,
    pub out: String,
    pub prefix: String,
    pub target: String,
    pub split_size: usize,
    pub vg_threads: usize,
    pub vg_binary: String,
    pub delimiter: char,
    pub keep_intermediate: bool,
    pub global: GlobalOpts,
}

Fields

reference: String

Reference FASTA file to use as source coordinates

input: String

Input file with annotations to lift (defaults to BED format)

bam: bool

Input file is in BAM format (default: BED format)

graph: String

Pangenome graph file in GBZ format

out: String

Output BED file with lifted annotations

prefix: String

panSN-spec prefix to add before graph injection (e.g., “HG002_2#0#”)

target: String

Target sample/haplotype name for surjection (e.g., “HG002_1”)

split_size: usize

Split contigs into multiple BAM records every N base pairs for graph injection

vg_threads: usize

Number of threads to use for vg operations

vg_binary: String

Path to vg binary (default: searches PATH)

delimiter: char

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

keep_intermediate: bool

Keep intermediate files for debugging

global: GlobalOpts

Trait Implementations

impl Args for PgLiftOptions

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 PgLiftOptions

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

Formats the value using the given formatter.

impl FromArgMatches for PgLiftOptions

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.