fibertools_rs/cli/
call_peaks_opts.rs

1use crate::utils::input_bam::InputBam;
2use clap::Args;
3use std::fmt::Debug;
4
5#[derive(Args, Debug)]
6pub struct CallPeaksOptions {
7    #[clap(flatten)]
8    pub input: InputBam,
9
10    /// BED file with shuffled fiber positions (from bedtools shuffle)
11    /// If not provided, will use all positions as real data (no FDR calculation)
12    #[clap(short, long)]
13    pub shuffled: Option<String>,
14
15    /// Output BED file with called peaks
16    #[clap(short, long, default_value = "-")]
17    pub out: String,
18
19    /// Maximum coverage threshold for filtering (optional)
20    #[clap(long)]
21    pub max_cov: Option<i32>,
22
23    /// Minimum coverage threshold for filtering (optional)
24    #[clap(long)]
25    pub min_cov: Option<i32>,
26
27    /// Number of standard deviations from median coverage to use for filtering (default: 5)
28    /// If set, will calculate median +/- (sd_cov * std_dev) and use those as min/max coverage
29    /// This overrides --max-cov and --min-cov if those are not explicitly set
30    #[clap(long, default_value = "5.0")]
31    pub sd_cov: f64,
32
33    /// Maximum FDR threshold for peak calling (ignored if --min-fire-frac is set)
34    #[clap(long, default_value = "0.05")]
35    pub max_fdr: f64,
36
37    /// Minimum fraction of fibers with FIREs required to call a peak
38    /// If set, skips FDR calculation and uses this threshold instead
39    /// For example, 0.5 means at least 50% of fibers must have a FIRE at the peak position
40    #[clap(long)]
41    pub min_fire_frac: Option<f64>,
42
43    /// Minimum fraction of fibers with FIREs required as an additional filter (applied WITH FDR)
44    /// Unlike --min-fire-frac, this is applied in addition to FDR filtering, not instead of it
45    /// For example, 0.3 means at least 30% of fibers must have a FIRE AND FDR must be <= max_fdr
46    #[clap(long, default_value = "0.1")]
47    pub min_fire_frac_filter: f64,
48
49    /// Minimum fraction of accessible bases in peak
50    #[clap(long, default_value = "0.0", hide = true)]
51    pub min_frac_accessible: f64,
52
53    /// Rolling window size for finding local maxima (in base pairs)
54    #[clap(long, default_value = "200")]
55    pub window_size: usize,
56
57    /// Minimum fraction of overlapping FIRE elements for merging peaks (Phase 2)
58    #[clap(long, default_value = "0.5")]
59    pub min_frac_overlap: f64,
60
61    /// Minimum reciprocal overlap for merging peaks (Phase 3)
62    #[clap(long, default_value = "0.75")]
63    pub min_reciprocal_overlap: f64,
64
65    /// High reciprocal overlap threshold for initial merging (Phase 1)
66    #[clap(long, default_value = "0.90")]
67    pub high_reciprocal_overlap: f64,
68
69    /// Maximum number of grouping iterations for merging
70    #[clap(long, default_value = "10")]
71    pub max_grouping_iterations: usize,
72
73    /// Skip the FDR table generation and use existing table
74    #[clap(long)]
75    pub fdr_table: Option<String>,
76
77    /// Output the FDR table to this file
78    #[clap(long)]
79    pub fdr_table_out: Option<String>,
80
81    /// Include nucleosome and MSP coverage in pileup (default: only FIRE coverage)
82    #[clap(long)]
83    pub include_nuc_msp: bool,
84
85    /// Include haplotype-specific calls
86    #[clap(long)]
87    pub haps: bool,
88
89    /// Minimum FIRE coverage required to calculate a score (default: 4)
90    #[clap(long, default_value = "4", hide = true)]
91    pub min_fire_coverage: i32,
92}
fibertools_rs/cli/call_peaks_opts.rs

fibertools_rs/cli/
call_peaks_opts.rs
