Struct Cli 

pub struct Cli {

    pub fasta: PathBuf,
    pub vcf: Option<PathBuf>,
    pub bam: Vec<PathBuf>,
    pub region: Option<String>,
    pub tag: Option<String>,
    pub annotations: Vec<PathBuf>,
    pub annotation_format: Option<String>,
    pub signals: Vec<PathBuf>,
    pub signal_format: Option<String>,
    pub links: Vec<PathBuf>,
    pub link_format: Option<String>,
    pub link_min_score: Option<f64>,
    pub light_mode: bool,
    pub log_level: String,
    pub config: Option<PathBuf>,
    pub snapshot_bed: Option<PathBuf>,
    pub snapshot_genes: Option<PathBuf>,
    pub snapshot_out: Option<PathBuf>,
    pub snapshot_format: String,
    pub snapshot_width: u32,
    pub snapshot_flank: f64,
    pub snapshot_theme: String,
    pub no_browser: bool,
    pub serve_port: u16,
}

Fields

fasta: PathBuf

Path to the reference genome FASTA file (must have a .fai index).

vcf: Option<PathBuf>

Path to a VCF file (must have a .tbi index). May be repeated in a future iteration; today only the first is honored.

bam: Vec<PathBuf>

Path to a BAM file (must have a .bai or .csi index). May be repeated to display multiple alignment tracks.

region: Option<String>

Initial region (e.g. “chr1:1000-2000”, “chr1:1000”, “chr1”).

tag: Option<String>

BAM tag to color reads by (two-character tag, e.g. “ha”).

annotations: Vec<PathBuf>

Path to a GFF3, GTF, BED, or narrowPeak/broadPeak annotation file. Format auto-detected by extension. May be repeated.

annotation_format: Option<String>

Override annotation format auto-detection (gff, gff3, gtf, bed, narrowpeak, or broadpeak). Applies to all -g files.

signals: Vec<PathBuf>

Path to a bigWig signal file (.bw / .bigwig). May be repeated.

signal_format: Option<String>

Override signal format auto-detection (currently only bigwig). Applies to all -s files.

links: Vec<PathBuf>

Path to a BEDPE link file (.bedpe / .bedpe.gz). May be repeated. Each file becomes its own track showing pairwise interactions (chromatin loops, enhancer-promoter, ChIA-PET, etc.).

link_format: Option<String>

Override link format auto-detection (currently only bedpe). Applies to all -l files.

link_min_score: Option<f64>

Drop links whose score column is below this value. Records without a score are unaffected.

light_mode: bool

Use light theme (for light-background terminals).

log_level: String

Logging level filter.

config: Option<PathBuf>

Optional override config path. Defaults to $XDG_CONFIG_HOME/igv-rs/config.toml.

snapshot_bed: Option<PathBuf>

Render snapshots for every region in this BED file (no TUI). Mutually exclusive with –snapshot-genes.

snapshot_genes: Option<PathBuf>

Render snapshots for every gene name in this newline-separated file (no TUI). Requires at least one -g/–annotation. Mutually exclusive with –snapshot-bed.

snapshot_out: Option<PathBuf>

Output directory for batch snapshots. Required when –snapshot-bed or –snapshot-genes is set.

snapshot_format: String

Output format for snapshots: svg (default) or png.

snapshot_width: u32

Image width in px for snapshots.

snapshot_flank: f64

Padding fraction added to each side of every batch region.

snapshot_theme: String

Snapshot color theme: igv (default) or tui.

no_browser: bool

Disable the B keystroke / browser launch (CI, headless servers).

serve_port: u16

TCP port for the browser-view HTTP server. 0 picks any free port.

Trait Implementations

impl Args for Cli

fn group_id() -> Option<Id>

Report the ArgGroup::id for this set of arguments

fn augment_args<'b>(__clap_app: Command) -> Command

Append to Command so it can instantiate Self via FromArgMatches::from_arg_matches_mut

fn augment_args_for_update<'b>(__clap_app: Command) -> Command

Append to Command so it can instantiate self via FromArgMatches::update_from_arg_matches_mut

impl CommandFactory for Cli

fn command<'b>() -> Command

Build a Command that can instantiate Self.

fn command_for_update<'b>() -> Command

Build a Command that can update self.

impl Debug for Cli

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

Formats the value using the given formatter.

impl FromArgMatches for Cli

fn from_arg_matches(__clap_arg_matches: &ArgMatches) -> Result<Self, Error>

Instantiate Self from ArgMatches, parsing the arguments as needed.

fn from_arg_matches_mut( __clap_arg_matches: &mut ArgMatches, ) -> Result<Self, Error>

Instantiate Self from ArgMatches, parsing the arguments as needed.

fn update_from_arg_matches( &mut self, __clap_arg_matches: &ArgMatches, ) -> Result<(), Error>

Assign values from ArgMatches to self.

fn update_from_arg_matches_mut( &mut self, __clap_arg_matches: &mut ArgMatches, ) -> Result<(), Error>

Assign values from ArgMatches to self.

impl Parser for Cli

fn parse() -> Self

Parse from std::env::args_os(), exit on error.

fn try_parse() -> Result<Self, Error>

Parse from std::env::args_os(), return Err on error.

fn parse_from<I, T>(itr: I) -> Self

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Parse from iterator, exit on error.

fn try_parse_from<I, T>(itr: I) -> Result<Self, Error>

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Parse from iterator, return Err on error.

fn update_from<I, T>(&mut self, itr: I)

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Update from iterator, exit on error.

fn try_update_from<I, T>(&mut self, itr: I) -> Result<(), Error>

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Update from iterator, return Err on error.