Struct MtxImport 

pub struct MtxImport {
    pub mtx: Box<str>,
    pub row: Option<Box<str>>,
    pub col: Option<Box<str>>,
    pub row_name_columns: usize,
    pub select_row_type: Box<str>,
    pub remove_row_type: Box<str>,
    pub hto_row_type: Box<str>,
}

A MatrixMarket matrix and its name files, as from_mtx reads them.

Fields

mtx: Box<str>

The matrix, .mtx.gz or .mtx: features as rows, cells as columns.

row: Option<Box<str>>

Feature names, one per line (.tsv.gz or .tsv). For 10x features.tsv[.gz] the columns are id, name, feature_type; the third, when present, is what the row-type filters read. A BED-shaped peaks file names its rows chr:start-end. None numbers them.

col: Option<Box<str>>

Cell barcodes, one per line; None numbers them.

row_name_columns: usize

How many columns of row name a feature: 2 joins id and name as id_name, 1 keeps the id.

select_row_type: Box<str>

Comma-separated patterns; a row is kept if its feature_type contains any of them (case-insensitive). Empty keeps every row.

remove_row_type: Box<str>

Comma-separated patterns; a row whose feature_type contains one goes, after select_row_type.

hto_row_type: Box<str>

The feature type of HTO (multiplexing) tags, such as Antibody Capture. When set, each cell is named barcode@{id}_{name} for the HTO row with its highest count, written to {stem}.barcode_to_hto.tsv.gz; HTO rows then go, and so do cells without any HTO count. Empty turns this off.

Implementations

impl MtxImport

pub fn new(mtx: &str) -> Self

mtx with the CLI’s defaults: rows numbered, 10x scRNA and ATAC rows kept (Gene Expression,Peaks), no HTO.

Trait Implementations

impl Clone for MtxImport

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 MtxImport

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

Formats the value using the given formatter.