From d8f3d70193cc8fad2b75adc6a30542f19d2b61eb Mon Sep 17 00:00:00 2001
From: Paul-Christian Volkmer <code@pcvolkmer.de>
Date: Mon, 11 Aug 2025 21:00:05 +0200
Subject: [PATCH] feat: add optional input file argument

---
 README.md   | 18 +++++++++++++++---
 src/cli.rs  |  5 ++++-
 src/main.rs | 29 ++++++++++++++++++++++++-----
 3 files changed, 43 insertions(+), 9 deletions(-)

diff --git a/README.md b/README.md
index 4dcd62e..952cc81 100644
--- a/README.md
+++ b/README.md
@@ -15,9 +15,10 @@ Commands:
   help      Print this message or the help of the given subcommand(s)
 
 Options:
-  -d, --decompress  decompress input as gzip compressed data
-  -h, --help        Print help
-  -V, --version     Print version
+  -i, --input <INPUT_FILE>  Input file (optional)
+  -d, --decompress          Decompress input as gzip compressed data
+  -h, --help                Print help
+  -V, --version             Print version
 ```
 
 ### Info
@@ -33,6 +34,11 @@ To use build-in decompression of input data, use the `--decompress`/`-d` option:
 ```shell
 cat file_fastq.gz | fastq-tools --decompress info
 ```
+Using optional input file argument:
+
+```shell
+fastq-tools --decompress --input file_fastq.gz info
+```
 
 This will result in output like
 
@@ -52,4 +58,10 @@ To use build-in decompression of input data, use the `--decompress`/`-d` option:
 
 ```shell
 cat file_fastq.gz | fastq-tools -d scramble | gzip > scrambled_fastq.gz
+```
+
+Using optional input file argument:
+
+```shell
+fastq-tools -d -i file_fastq.gz scramble | gzip > scrambled_fastq.gz
 ```
\ No newline at end of file
diff --git a/src/cli.rs b/src/cli.rs
index cf554da..780eb9b 100644
--- a/src/cli.rs
+++ b/src/cli.rs
@@ -1,4 +1,5 @@
 use clap::{Parser, Subcommand};
+use std::path::PathBuf;
 
 #[derive(Parser)]
 #[command(author, version, about, long_about = None)]
@@ -6,10 +7,12 @@ use clap::{Parser, Subcommand};
 pub struct Args {
     #[command(subcommand)]
     pub(crate) command: Command,
+    #[arg(short = 'i', long = "input", help = "Input file (optional)")]
+    pub(crate) input_file: Option<PathBuf>,
     #[arg(
         short = 'd',
         long = "decompress",
-        help = "decompress input as gzip compressed data"
+        help = "Decompress input as gzip compressed data"
     )]
     pub(crate) decompress: bool,
 }
diff --git a/src/main.rs b/src/main.rs
index 35326fa..48a7cb7 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -8,6 +8,7 @@ use console::Style;
 use flate2::read::GzDecoder;
 use itertools::Itertools;
 use regex::Regex;
+use std::fs::File;
 use std::io::{BufRead, BufReader};
 
 fn scramble_sequence(value: &str, seed: u32) -> String {
@@ -55,25 +56,43 @@ fn scramble_sequence(value: &str, seed: u32) -> String {
 
 fn main() {
     let args = Args::parse();
-    let stdin = std::io::stdin();
+    let input: Box<dyn BufRead> = match args.input_file {
+        Some(input_file) => {
+            let file = match File::open(input_file) {
+                Ok(file) => file,
+                _ => {
+                    println!(
+                        "{}\n",
+                        Style::new()
+                            .bold()
+                            .red()
+                            .apply_to("🔥 Cannot open input file")
+                    );
+                    return;
+                }
+            };
+            Box::new(BufReader::new(file))
+        }
+        _ => Box::new(BufReader::new(std::io::stdin())),
+    };
 
     match &args.command {
         Command::Info => {
             if args.decompress {
-                let gz_decoder = GzDecoder::new(stdin);
+                let gz_decoder = GzDecoder::new(input);
                 let buf_reader = BufReader::new(gz_decoder);
                 info(buf_reader)
             } else {
-                info(BufReader::new(stdin))
+                info(BufReader::new(input))
             }
         }
         Command::Scramble => {
             if args.decompress {
-                let gz_decoder = GzDecoder::new(stdin);
+                let gz_decoder = GzDecoder::new(input);
                 let buf_reader = BufReader::new(gz_decoder);
                 scramble(buf_reader)
             } else {
-                scramble(BufReader::new(stdin))
+                scramble(BufReader::new(input))
             }
         }
     }