Struct QcArgs 

pub struct QcArgs {

    pub no_qc: bool,
    pub qc_mads: f32,
    pub qc_min_cell_nnz: usize,
    pub qc_min_counts: f32,
    pub qc_mito_pattern: Option<String>,
    pub qc_mito_max_frac: Option<f32>,
    pub qc_ribo_pattern: Option<String>,
    pub qc_ribo_max_frac: Option<f32>,
    pub qc_feature_min_cells: usize,
    pub qc_report: Option<Box<str>>,
    pub qc_histogram: bool,
    pub qc_mad_on_genes: bool,
    pub qc_mad_on_counts: bool,
    pub qc_auto_cutoff: bool,
}

Clap surface for cell QC, shared by senna and pinto subcommands.

Cell QC is ON by default and CAN DROP CELLS (columns). Low-quality cells are removed: near-empty cells are omitted from the per-cell outputs, and robust (MAD) outlier cells are excluded from training entirely. As a result, the per-cell output files (*.latent.parquet, *.cell_proj.parquet, *.cell_to_pb.parquet, *.cell_embedding.parquet, pinto propensity, etc.) may contain fewer rows (cells) than the input — do not assume a 1:1, positional correspondence with the input barcodes; always join by the cell name/barcode column. Pass --no-qc to disable and keep every cell, or --qc-report <path> to dump the per-cell keep/drop flags. (Feature/row QC is OFF unless --qc-feature-min-cells is set.)

Fields

no_qc: bool

Disable cell QC entirely (keep every input cell).

qc_mads: f32

MAD multiplier for the robust outlier band; smaller = drops more cells.

qc_min_cell_nnz: usize

qc_min_counts: f32

qc_mito_pattern: Option<String>

qc_mito_max_frac: Option<f32>

Hard max mitochondrial fraction (0..1).

qc_ribo_pattern: Option<String>

Regex over feature names selecting ribosomal genes.

qc_ribo_max_frac: Option<f32>

Hard max ribosomal fraction (0..1).

qc_feature_min_cells: usize

qc_report: Option<Box<str>>

qc_histogram: bool

qc_mad_on_genes: bool

qc_mad_on_counts: bool

qc_auto_cutoff: bool

Implementations

impl QcArgs

pub fn to_config(&self) -> Option<QcConfig>

QC config, or None under --no-qc.

Trait Implementations

impl Args for QcArgs

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 QcArgs

fn clone(&self) -> Self

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for QcArgs

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

Formats the value using the given formatter.

impl<'de> Deserialize<'de> for QcArgs

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl FromArgMatches for QcArgs

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 Serialize for QcArgs

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error>

where __S: Serializer,

Serialize this value into the given Serde serializer.