cyto_cli/map/
mod.rs

1pub mod crispr;
2pub mod gex;
3mod input;
4mod options;
5mod runtime;
6
7pub use crispr::ArgsCrispr;
8pub use gex::ArgsGex;
9pub use input::MultiPairedInput;
10pub use options::MapOptions;
11pub use runtime::RuntimeOptions;
12
13use std::path::PathBuf;
14
15use anyhow::Result;
16use clap::Subcommand;
17
18#[derive(Subcommand, Debug)]
19pub enum MapCommand {
20    /// Map sequences to a Flex GEX library (v2)
21    Gex(ArgsGex),
22    /// Map sequences to a Flex CRISPR library (v2)
23    Crispr(ArgsCrispr),
24}
25
26impl MapCommand {
27    pub fn validate_outdir(&self) -> Result<()> {
28        match self {
29            MapCommand::Gex(args) => args.output.validate_outdir(),
30            MapCommand::Crispr(args) => args.output.validate_outdir(),
31        }
32    }
33
34    pub fn log_path(&self) -> PathBuf {
35        match self {
36            MapCommand::Gex(args) => args.output.log_path(),
37            MapCommand::Crispr(args) => args.output.log_path(),
38        }
39    }
40}
41
42pub const GEOMETRY_GEX_FLEX_V1: &str = "[barcode][umi:12] | [gex][:18][probe]";
43pub const GEOMETRY_GEX_FLEX_V2: &str = "[barcode][umi:12][:10][probe] | [gex]";
44pub const GEOMETRY_CRISPR_FLEX_V1: &str = "[barcode][umi:12] | [probe][anchor][protospacer]";
45pub const GEOMETRY_CRISPR_FLEX_V2: &str =
46    "[barcode][umi:12][:10][probe] | [:14][anchor][protospacer]";
47pub const GEOMETRY_CRISPR_PROPERSEQ: &str = "[barcode][umi:12] | [:18][probe][anchor][protospacer]";
cyto_cli/map/mod.rs

cyto_cli/map/
mod.rs
