feat: add build-in gzip decompression

Cargo.toml

@@ -12,3 +12,4 @@ regex = "1.11"
 clap = {  version = "4.5", features = ["color", "derive"]}
 console = "0.16"
 itertools = "0.14"
+flate2 = "1.1"

README.md

@@ -6,6 +6,20 @@ Application to show information about and scramble FASTQ files to provide non-se
 
 This application provides the following subcommands
 
+```
+Usage: fastq-tools [OPTIONS] <COMMAND>
+
+Commands:
+  info      Show information about input
+  scramble  Scramble input data
+  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
+```
+
 ### Info
 
 To show information about compressed FASTQ files use:
@@ -14,6 +28,12 @@ To show information about compressed FASTQ files use:
 cat file_fastq.gz | gzip -d | fastq-tools info
 ```
 
+To use build-in decompression of input data, use the `--decompress`/`-d` option:
+
+```shell
+cat file_fastq.gz | fastq-tools --decompress info
+```
+
 This will result in output like
 
 ![Info subcommand](docs/info_subcommand.jpg)
@@ -26,4 +46,10 @@ To scramble compressed FASTQ files use:
 cat file_fastq.gz | gzip -d | fastq-tools scramble | gzip > scrambled_fastq.gz
 ```
 
-This will scramble headers and sequences and write the output into `scrambled_fastq.gz`.
+This will scramble headers and sequences and write the output into `scrambled_fastq.gz`.
+
+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
+```

src/cli.rs

@@ -6,10 +6,18 @@ use clap::{Parser, Subcommand};
 pub struct Args {
     #[command(subcommand)]
     pub(crate) command: Command,
+    #[arg(
+        short = 'd',
+        long = "decompress",
+        help = "decompress input as gzip compressed data"
+    )]
+    pub(crate) decompress: bool,
 }
 
 #[derive(Subcommand)]
 pub enum Command {
+    #[command(about = "Show information about input")]
     Info,
+    #[command(about = "Scramble input data")]
     Scramble,
 }

src/main.rs

@@ -5,8 +5,10 @@ use crate::cli::{Args, Command};
 use crate::fastq::{Header, Pair};
 use clap::Parser;
 use console::Style;
+use flate2::read::GzDecoder;
 use itertools::Itertools;
 use regex::Regex;
+use std::io::{BufRead, BufReader};
 
 fn scramble_sequence(value: &str, seed: u32) -> String {
     let ahead_1 = Regex::new(r"T([ACG])").unwrap();
@@ -53,22 +55,37 @@ fn scramble_sequence(value: &str, seed: u32) -> String {
 
 fn main() {
     let args = Args::parse();
+    let stdin = std::io::stdin();
 
     match &args.command {
-        Command::Info => info(),
-        Command::Scramble => scramble(),
+        Command::Info => {
+            if args.decompress {
+                let gz_decoder = GzDecoder::new(stdin);
+                let buf_reader = BufReader::new(gz_decoder);
+                info(buf_reader)
+            } else {
+                info(BufReader::new(stdin))
+            }
+        }
+        Command::Scramble => {
+            if args.decompress {
+                let gz_decoder = GzDecoder::new(stdin);
+                let buf_reader = BufReader::new(gz_decoder);
+                scramble(buf_reader)
+            } else {
+                scramble(BufReader::new(stdin))
+            }
+        }
     }
 
     println!()
 }
 
-fn scramble() {
-    let stdin = std::io::stdin();
+fn scramble(mut reader: impl BufRead) {
     let mut buf = String::new();
 
     let mut line = 1;
-
-    while let Ok(n) = stdin.read_line(&mut buf) {
+    while let Ok(n) = reader.read_line(&mut buf) {
         if n == 0 {
             break;
         }
@@ -88,8 +105,7 @@ fn scramble() {
     }
 }
 
-fn info() {
-    let stdin = std::io::stdin();
+fn info(mut reader: impl BufRead) {
     let mut buf = String::new();
 
     let mut headers = vec![];
@@ -101,7 +117,7 @@ fn info() {
     let error_style = Style::new().bold().red();
 
     let mut line = 1;
-    while let Ok(n) = stdin.read_line(&mut buf) {
+    while let Ok(n) = reader.read_line(&mut buf) {
         if n == 0 {
             break;
         }
@@ -136,6 +152,11 @@ fn info() {
         buf.clear();
     }
 
+    if line == 1 {
+        println!("{}", error_style.apply_to("🔥 No valid input"));
+        return;
+    }
+
     if line % 4 != 1 {
         println!(
             "{}",