cyto_cli/ibu/
barcode.rs

1use std::path::Path;
2
3use super::IbuInput;
4
5use clap::Parser;
6
7#[derive(Parser, Debug)]
8pub struct ArgsBarcode {
9    #[clap(flatten)]
10    pub input: IbuInput,
11
12    #[clap(flatten)]
13    pub options: OptionsBarcode,
14}
15impl ArgsBarcode {
16    pub fn from_wf_path<P: AsRef<Path>>(
17        input_path: &str,
18        output_path: &str,
19        whitelist: &str,
20        bc_log: P,
21        exact: bool,
22        skip_second_pass: bool,
23    ) -> Self {
24        Self {
25            input: IbuInput::from_path(input_path),
26            options: OptionsBarcode {
27                whitelist: whitelist.to_string(),
28                exact,
29                skip_second_pass,
30                include: false,
31                output: Some(output_path.to_string()),
32                log: Some(bc_log.as_ref().display().to_string()),
33            },
34        }
35    }
36}
37
38#[derive(Parser, Debug)]
39#[clap(next_help_heading = "Barcode Correction Options")]
40pub struct OptionsBarcode {
41    /// Path of the whitelist file
42    ///
43    /// This is a file containing a single nucleotide sequence per line
44    ///
45    /// Compression supported for: [gzip, bzip, lzma, zstd]
46    #[clap(short = 'w', long)]
47    pub whitelist: String,
48
49    /// Exact match only
50    ///
51    /// If this flag is present, only exact matches will be accepted.
52    #[clap(long = "bc-exact")]
53    pub exact: bool,
54
55    /// Skip second pass correction
56    ///
57    /// Second pass correction is enabled by default and collapses cell barcodes into the maximum abundance ambiguous parent
58    #[clap(short = 's', long)]
59    pub skip_second_pass: bool,
60
61    /// Include ambiguous or non-whitelist sequences
62    ///
63    /// If this flag is present, sequences that are
64    /// not within the distance threshold of a whitelist sequence
65    /// or are ambiguously distant from multiple whitelist sequences
66    /// will be included in the output.
67    #[clap(short = 'I', long)]
68    pub include: bool,
69
70    /// Output file to write to [default=stdout]
71    #[clap(short, long)]
72    pub output: Option<String>,
73
74    /// Output file to write statistics to [default=stderr]
75    ///
76    /// Will output as json
77    #[clap(short, long)]
78    pub log: Option<String>,
79}
cyto_cli/ibu/barcode.rs

cyto_cli/ibu/
barcode.rs
