Struct PgInjectOptions 

pub struct PgInjectOptions {
    pub reference: String,
    pub out: String,
    pub split_size: usize,
    pub uncompressed: bool,
    pub bed: Option<String>,
    pub extract: bool,
    pub header_out: Option<String>,
    pub global: GlobalOpts,
    pub pansn: PansnParameters,
}

Fields

reference: String

Reference FASTA file to create mock BAM from (supports .gz/.bgz compression)

out: String

Output BAM file

split_size: usize

Split contigs into multiple BAM records every N base pairs (0 = no splitting)

uncompressed: bool

Uncompressed BAM output (default: compressed)

bed: Option<String>

Optional BED file with annotations to add to mock BAM records

extract: bool

Extract BED annotations from an annotated BAM file (reverses injection)

header_out: Option<String>

Additionally write the output BAM header to this file

global: GlobalOpts

pansn: PansnParameters

Trait Implementations

impl Args for PgInjectOptions

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 PgInjectOptions

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

Formats the value using the given formatter.

impl FromArgMatches for PgInjectOptions

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.