Struct ArgsWorkflow 

pub struct ArgsWorkflow {

    pub skip_barcode: bool,
    pub skip_umi: bool,
    pub skip_reads: bool,
    pub no_filter: bool,
    pub keep_unfiltered: bool,
    pub keep_ibu: bool,
    pub skip_assignment: bool,
    pub sort_in_memory: bool,
    pub memory_limit: String,
    pub bc_exact: bool,
    pub skip_bc_second_pass: bool,
    pub whitelist: String,
    pub format: CountFormat,
}

Fields

skip_barcode: bool

Skip barcode correction step

skip_umi: bool

Skip UMI correction step

skip_reads: bool

Skip reads/umi saturation step

no_filter: bool

Skip EmptyDrops filtering step (GEX)

Only used when format is h5ad

keep_unfiltered: bool

Keep the unfiltered h5ad file (GEX)

Only used when format is h5ad

keep_ibu: bool

Keep the IBU file(s) after counting

skip_assignment: bool

Skip CRISPR-barcode assignment step (CRISPR)

Only used when format is h5ad

sort_in_memory: bool

Sort in memory instead of using disk

memory_limit: String

Memory limit for sorting (ignored if sort_in_memory is true)

bc_exact: bool

Exact barcode matching only

Default allows barcode correction of 1 unambiguous mismatch from whitelist

skip_bc_second_pass: bool

Skip barcode correction second pass step.

This skips recovery of ambiguous one-offs barcodes by parent abundance.

whitelist: String

Cell Barcode Whitelist

format: CountFormat

Implementations

impl ArgsWorkflow

pub fn validate_requirements(&self, mode: WorkflowMode) -> Result<()>

pub fn mtx(&self) -> bool

Check whether the workflow should output mtx files

This is true if the format is mtx or h5ad but mtx is consumed by h5ad

pub fn to_h5ad(&self) -> bool

Check whether the workflow should output h5ad files

Trait Implementations

impl Args for ArgsWorkflow

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 CommandFactory for ArgsWorkflow

fn command<'b>() -> Command

Build a Command that can instantiate Self.

fn command_for_update<'b>() -> Command

Build a Command that can update self.

impl Debug for ArgsWorkflow

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

Formats the value using the given formatter.

impl FromArgMatches for ArgsWorkflow

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.

impl Parser for ArgsWorkflow

fn parse() -> Self

Parse from std::env::args_os(), exit on error.

fn try_parse() -> Result<Self, Error>

Parse from std::env::args_os(), return Err on error.

fn parse_from<I, T>(itr: I) -> Self

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Parse from iterator, exit on error.

fn try_parse_from<I, T>(itr: I) -> Result<Self, Error>

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Parse from iterator, return Err on error.

fn update_from<I, T>(&mut self, itr: I)

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Update from iterator, exit on error.

fn try_update_from<I, T>(&mut self, itr: I) -> Result<(), Error>

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Update from iterator, return Err on error.