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use barbell::annotate::annotator::*;
use barbell::annotate::barcodes::BarcodeType;
use barbell::filter::filter::filter_from_text_file;
use barbell::inspect::inspect;
use barbell::kits::use_kit::demux_using_kit;
use barbell::trim::trim::{LabelSide, trim_matches};
use clap::{Parser, Subcommand};
use colored::*;
#[derive(Parser)]
#[command(author, version, about, long_about = None)]
struct Cli {
#[command(subcommand)]
command: Commands,
}
#[derive(Subcommand)]
enum UtilsCommands {
/// Group raw reads by label without trimming
Pull {
/// Input filtered annotation file
#[arg(short = 'i', long)]
input: String,
/// Read FASTQ file
#[arg(short = 'r', long)]
reads: String,
/// Output folder path for grouped reads
#[arg(short = 'o', long)]
output: String,
/// Disable label in output filenames
#[arg(long, default_value_t = false)]
no_label: bool,
/// Disable orientation in output filenames
#[arg(long, default_value_t = false)]
no_orientation: bool,
/// Disable flank in output filenames
#[arg(long, default_value_t = false)]
no_flanks: bool,
/// Sort barcode labels in output filenames
#[arg(long, default_value_t = false)]
sort_labels: bool,
/// Only keep left or right label in output filenames
#[arg(long, conflicts_with = "sort_labels")]
only_side: Option<LabelSide>,
/// Write ids of reads with no annotations to this file
#[arg(long)]
failed_out: Option<String>,
},
}
#[derive(Subcommand)]
enum Commands {
/// Annotate FASTQ files with barcode information
Annotate {
/// Input FASTQ file
#[arg(short = 'i', long)]
input: String,
/// Number of threads
#[arg(short = 't', long, default_value_t = 10)]
threads: usize,
/// Output file path
#[arg(short = 'o', long, default_value = "output.tsv")]
output: String,
/// Query files (comma-separated paths)
#[arg(short = 'q', long, required_unless_present = "kit")]
queries: Option<String>,
/// Barcode types (comma-separated: Ftag,Rtag) matching your query file (-q)
#[arg(short = 'b', long, default_value = "Ftag")]
barcode_types: String,
/// Kit name (e.g. SQK-RBK114-24). Conflicts with --queries/--barcode-types
#[arg(long, conflicts_with = "queries", conflicts_with = "barcode_types")]
kit: Option<String>,
/// Flank maximum erors in flank, ONLY set manually when you know what you are doing
#[arg(long = "flank-max-errors", value_name = "INT")]
flank_max_errors: Option<usize>,
/// Enable verbose output for debugging
#[arg(long, default_value_t = false)]
verbose: bool,
/// Barcode: fraction compared to 'perfect' match score for top candidate
#[arg(long = "min-score", default_value_t = 0.2)]
min_score: f64,
/// Barcode: fraction difference between top 2 candidates
#[arg(long = "min-score-diff", default_value_t = 0.1)]
min_score_diff: f64,
/// Also use extended templates (if using kit), i.e. detect fusions, breaks, etc. (slower)
#[arg(long, default_value_t = false)]
use_extended: bool,
/// Edit cost beyond read boundaries
#[arg(long = "alpha", default_value_t = 0.4)]
alpha: f32,
},
/// Filter annotation files based on pattern
Filter {
/// Input annotation file
#[arg(short = 'i', long, required = true)]
input: String,
/// Output filtered file path
#[arg(short = 'o', long, required = true)]
output: String,
/// File containing patterns to filter by
#[arg(short = 'f', long, required = true)]
file: String,
/// Write dropped read annotation to this file
#[arg(long)]
dropped: Option<String>,
},
/// Trim and sort reads based on filtered annotations
Trim {
/// Input filtered annotation file
#[arg(short = 'i', long)]
input: String,
/// Read FASTQ file
#[arg(short = 'r', long)]
reads: String,
/// Output folder path for trimmed reads
#[arg(short = 'o', long)]
output: String,
/// Disable label in output filenames
#[arg(long, default_value_t = false)]
no_label: bool,
/// Disable orientation in output filenames
#[arg(long, default_value_t = false)]
no_orientation: bool,
/// Disable flank in output filenames
#[arg(long, default_value_t = false)]
no_flanks: bool,
/// Sort barcode labels in output filenames
#[arg(long, default_value_t = false)]
sort_labels: bool,
/// Only keep left or right label in output filenames
#[arg(long, conflicts_with = "sort_labels")]
only_side: Option<LabelSide>,
/// Write ids of failed trimmed reads to this file
#[arg(long)]
failed_out: Option<String>,
},
/// View most common patterns in annotation
Inspect {
/// Input filtered annotation file
#[arg(short = 'i', long)]
input: String,
/// Top N
#[arg(short = 'n', long, default_value_t = 10)]
top_n: usize,
/// Write pattern for each read to this file (optional)
#[arg(short = 'o', long)]
read_pattern_out: Option<String>,
/// To summarize results we uses "buckets", such that matches 100 and 103 from the start end up in the same bucket
#[arg(short = 's', long = "bucket-size", default_value_t = 250)]
bucket_size: usize,
},
/// Run a preset
Kit {
/// Kit to use (e.g. SQK-RBK114-24)
#[arg(short = 'k', long)]
kit: String,
/// Input FASTQ file
#[arg(short = 'i', long)]
input: String,
/// Number of threads
#[arg(short = 't', long, default_value_t = 10)]
threads: usize,
/// Output folder
#[arg(short = 'o', long)]
output: String,
/// Add more 'risky' patterns to demuxing to maximize assigned reads
#[arg(long, default_value_t = false)]
maximize: bool,
/// Enable verbose output for debugging
#[arg(long, default_value_t = false)]
verbose: bool,
/// Fraction compared to 'perfect' match score for top candidate
#[arg(long = "min-score", default_value_t = 0.2)]
min_score: f64,
/// Fraction difference between top 2 candidates
#[arg(long = "min-score-diff", default_value_t = 0.1)]
min_score_diff: f64,
/// Flank maximum erors in flank, ONLY set manually when you know what you are doing
#[arg(long = "flank-max-errors", value_name = "INT")]
flank_max_errors: Option<usize>,
/// Write ids of failed trimmed reads to this file
#[arg(long)]
failed_out: Option<String>,
/// Also use extended templates (if using kit), i.e. detect fusions, breaks, etc. (slower)
#[arg(long, default_value_t = false)]
use_extended: bool,
/// Edit cost beyond read boundaries
#[arg(long = "alpha", default_value_t = 0.4)]
alpha: f32,
},
}
fn main() {
// Make sure that AVX2 is supported by the current CPU if it was used during compilation.
ensure_simd::ensure_simd();
print_banner();
let cli = Cli::parse();
match &cli.command {
Commands::Annotate {
input,
threads,
output,
queries,
barcode_types,
kit,
flank_max_errors,
verbose,
min_score,
min_score_diff,
use_extended,
alpha,
} => {
println!("{}", "Starting annotation...".green());
if let Some(kit_name) = kit.as_ref() {
match annotate_with_kit(
input,
output,
kit_name.as_str(),
*flank_max_errors,
*alpha,
*threads as u32,
*verbose,
*min_score,
*min_score_diff,
*use_extended,
) {
Ok(_) => println!("{}", "Annotation complete!".green()),
Err(e) => println!("{} {}", "Error during processing:".red(), e),
}
return;
}
// Split comma-separated query paths into Vec<String>
let queries_value = queries
.as_ref()
.expect("--queries is required unless --kit is provided");
let query_files: Vec<String> = queries_value
.split(',')
.map(|s| s.trim().to_string())
.collect();
let query_files_refs: Vec<&str> = query_files.iter().map(|s| s.as_str()).collect();
// Parse barcode types
let barcode_types_vec: Vec<BarcodeType> = barcode_types
.split(',')
.map(|s| match s.trim() {
"Ftag" => BarcodeType::Ftag,
"Rtag" => BarcodeType::Rtag,
_ => {
panic!("Unknown barcode type: {s}, use one of: Ftag, Rtag")
}
})
.collect();
match annotate_with_files(
input,
query_files_refs,
barcode_types_vec,
output,
*flank_max_errors,
*alpha,
*threads as u32,
*verbose,
*min_score,
*min_score_diff,
) {
// Convert fractions to raw scores
Ok(_) => println!("{}", "Annotation complete!".green()),
Err(e) => println!("{} {}", "Error during processing:".red(), e),
}
}
Commands::Filter {
input,
output,
file,
dropped,
} => {
println!("{}", "Starting filtering...".green());
match filter_from_text_file(input, file, output, dropped.as_deref()) {
Ok(_) => println!("{}", "Filtering successful!".green()),
Err(e) => println!("{} {}", "Filtering failed:".red(), e),
}
}
Commands::Trim {
input,
reads,
output,
no_label,
no_orientation,
no_flanks,
sort_labels,
only_side,
failed_out,
} => {
println!("{}", "Starting trimming...".green());
trim_matches(
input,
reads,
output,
!no_label,
!no_orientation,
!no_flanks,
*sort_labels,
*only_side,
failed_out.clone(),
true, // Maybe make this optional but dont see a reason why you would not want this
);
}
Commands::Inspect {
input,
top_n,
read_pattern_out,
bucket_size,
} => {
println!("{}", "Inspecting...".green());
match inspect::inspect(input, *top_n, read_pattern_out.clone(), *bucket_size) {
Ok(_) => println!("{}", "Inspection complete!".green()),
Err(e) => println!("{} {}", "Inspection failed:".red(), e),
}
}
Commands::Kit {
kit,
input,
threads,
output,
maximize,
verbose,
min_score,
min_score_diff,
flank_max_errors,
failed_out,
use_extended,
alpha,
} => {
demux_using_kit(
kit.as_str(),
input,
*threads,
output,
*maximize,
*verbose,
*min_score,
*min_score_diff,
*flank_max_errors,
failed_out.clone(),
*use_extended,
*alpha,
);
}
}
}
fn print_banner() {
println!(
"{}",
r#"
██████╗ █████╗ ██████╗ ██████╗ ███████╗██╗ ██╗
██╔══██╗██╔══██╗██╔══██╗██╔══██╗██╔════╝██║ ██║
██████╔╝███████║██████╔╝██████╔╝█████╗ ██║ ██║
██╔══██╗██╔══██║██╔══██╗██╔══██╗██╔══╝ ██║ ██║
██████╔╝██║ ██║██║ ██║██████╔╝███████╗███████╗███████╗
╚═════╝ ╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚══════╝╚══════╝╚══════╝
"#
.blue()
);
println!(
"{}",
" [===]------------------------------------------[===] ".bright_yellow()
);
}