cyto_cli/map/
map.rs

1use clap::Parser;
2
3#[derive(Debug, Clone, Copy, Parser)]
4#[clap(next_help_heading = "Mapping Options")]
5pub struct MapOptions {
6    /// Use exact matching for sequences and/or probes.
7    ///
8    /// Default allows for unambiguous 1-hamming distance mismatches
9    #[clap(short = 'x', long)]
10    pub exact_matching: bool,
11
12    /// Skip quality check for UMI sequences
13    ///
14    /// Default removes UMIs if a quality score is below a fixed threshold
15    #[clap(long)]
16    pub no_umi_quality_check: bool,
17
18    /// Never remap sequences and/or probes with +-1 position adjustment
19    #[clap(long)]
20    no_remap: bool,
21}
22impl MapOptions {
23    pub fn adjustment(&self) -> bool {
24        !self.no_remap
25    }
26    pub fn umi_quality_removal(&self) -> bool {
27        !self.no_umi_quality_check
28    }
29}
cyto_cli/map/map.rs

cyto_cli/map/
map.rs
