feat(main): Add command for generating completion files

Cargo.toml

@@ -30,13 +30,9 @@ codegen-units = 1
 
 [dependencies]
 anyhow = { version = "1.0" }
-clap = { version = "4.4.7", features = [
-    "wrap_help",
-    "derive",
-    "color",
-    "cargo",
-] }
+clap = { version = "4.4.7", features = ["wrap_help", "derive", "cargo"] }
 clap-verbosity-flag = "2.1.0"
+clap_complete = "4.4"
 colored = "2"
 env_logger = "0.10"
 human-panic = "1.2.1"

src/main.rs

@@ -1,34 +1,44 @@
-use clap::{Parser, Subcommand};
+use clap::{Command, CommandFactory, Parser, Subcommand, ValueHint};
 use env_logger::Builder;
 use human_panic::setup_panic;
 use log::info;
 use log::LevelFilter;
 use std::path::PathBuf;
 
+use clap_complete::{generate, Generator, Shell};
+use std::io;
+
 mod extract;
 mod fa2fq;
 mod fq2fa;
 mod index;
 mod rsoft;
 
-#[derive(Parser)]
+#[derive(Parser, Debug)]
 #[command(author, version, about, long_about = None)]
 #[command(propagate_version = true)]
 struct Cli {
-    #[command(flatten)]
-    verbose: clap_verbosity_flag::Verbosity,
+    // If provided, outputs the completion file for given shell
+    #[arg(long = "generate", value_enum)]
+    generator: Option<Shell>,
 
     #[command(subcommand)]
     command: Option<Commands>,
+
+    #[command(flatten)]
+    verbose: clap_verbosity_flag::Verbosity,
 }
 
-#[derive(Subcommand)]
+#[derive(Subcommand, Debug)]
 enum Commands {
     /// Extract reads from a BAM file
+    #[command(visible_alias = "e")]
     Extract {
         /// Read IDs
+        #[arg(value_hint = ValueHint::FilePath)]
         readids: String,
         /// Bam input file
+        #[arg(value_hint = ValueHint::FilePath)]
         input: PathBuf,
 
         /// Is the output file a BAM file
@@ -39,28 +49,32 @@ enum Commands {
     /// Index a BAM file
     Index {
         /// Bam input file
+        #[arg(value_hint = ValueHint::FilePath)]
         input: PathBuf,
     },
 
     /// Convert a FASTA file to FASTQ
     Fa2fq {
         /// fasta input file
+        #[arg(value_hint = ValueHint::FilePath)]
         input: PathBuf,
     },
 
     /// Convert a FASTQ file to FASTA
     Fq2fa {
         /// fastq input file
+        #[arg(value_hint = ValueHint::FilePath)]
         input: PathBuf,
     },
 
     /// Create softlinks to files with same suffix in one directory recursively
     Rsoft {
         /// The directory to search
+        #[arg(value_hint = ValueHint::FilePath)]
         source: PathBuf,
 
         /// The directory to create the softlinks. default is current directory
-        #[arg(short = 't')]
+        #[arg(short = 't', value_hint = ValueHint::FilePath)]
         target: Option<PathBuf>,
 
         /// The suffix of the files to link. default is all files
@@ -69,6 +83,10 @@ enum Commands {
     },
 }
 
+fn print_completions<G: Generator>(gen: G, cmd: &mut Command) {
+    generate(gen, cmd, cmd.get_name().to_string(), &mut io::stdout());
+}
+
 fn main() {
     setup_panic!();
 
@@ -88,6 +106,13 @@ fn main() {
     }
     log_builder.init();
 
+    if let Some(generator) = cli.generator {
+        let mut cmd = Cli::command();
+        info!("Generating completion file for {generator:?}...");
+        print_completions(generator, &mut cmd);
+        return;
+    }
+
     // You can check for the existence of subcommands, and if found use their
     // matches just as you would the top level cmd
     match &cli.command {