Struct ArgsCount 

pub struct ArgsCount {
    pub input: IbuInput,
    pub output: Option<String>,
    pub mtx: bool,
    pub num_threads: usize,
    pub compressed: bool,
    pub features: Option<String>,
    pub feature_col: usize,
    pub suffix: Option<String>,
}

Fields

input: IbuInput

output: Option<String>

Output file to write to [default=stdout]

mtx: bool

Output mtx format. Will treat output as a directory and create 3 files:

(1) barcodes.txt.gz (2) features.txt.gz (3) matrix.mtx.gz

num_threads: usize

Number of threads to use in counting

compressed: bool

Keep the barcode values 2bit compressed in the output

features: Option<String>

File containing the index features

If this is provided the index features names will be output instead of their index values

feature_col: usize

The column in the feature table to aggregate reads over - skips aggregation if this is zero

suffix: Option<String>

Suffix to append to cell barcodes

example: {barcode}-{suffix}

Implementations

impl ArgsCount

pub fn from_wf_path<P: AsRef<Path>>( sort_path: &str, out_path: P, features_path: P, num_threads: usize, mtx: bool, suffix: Option<String>, ) -> Self

Trait Implementations

impl Args for ArgsCount

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 ArgsCount

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 ArgsCount

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

Formats the value using the given formatter.

impl FromArgMatches for ArgsCount

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 ArgsCount

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.