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//! Input format detection and selection.
//!
//! This module provides types for specifying and auto-detecting input file formats
//! (FASTA or FASTQ).
use clap::ValueEnum;
use std::ffi::OsStr;
use std::path::Path;
/// Input sequence file format.
///
/// Used to specify the format of input files. When set to `Auto`, the format
/// is detected from the file extension.
#[derive(Debug, Clone, Copy, PartialEq, Eq, Default, ValueEnum)]
pub enum SequenceFormat {
/// Auto-detect format from file extension.
///
/// Detection rules:
/// - `.fq`, `.fastq`, `.fq.gz`, `.fastq.gz` -> FASTQ
/// - `.fa`, `.fasta`, `.fna`, `.fa.gz`, `.fasta.gz`, `.fna.gz` -> FASTA
/// - Unknown or stdin -> FASTA (default)
#[default]
Auto,
/// FASTA format (`.fa`, `.fasta`, `.fna`).
Fasta,
/// FASTQ format (`.fq`, `.fastq`).
Fastq,
}
impl SequenceFormat {
/// Detects the sequence format from a file path's extension.
///
/// Handles gzip-compressed files by stripping the `.gz` extension first.
///
/// # Examples
///
/// ```
/// use kmerust::format::SequenceFormat;
/// use std::path::Path;
///
/// assert_eq!(SequenceFormat::from_extension(Path::new("reads.fq")), SequenceFormat::Fastq);
/// assert_eq!(SequenceFormat::from_extension(Path::new("reads.fastq.gz")), SequenceFormat::Fastq);
/// assert_eq!(SequenceFormat::from_extension(Path::new("genome.fa")), SequenceFormat::Fasta);
/// assert_eq!(SequenceFormat::from_extension(Path::new("genome.fasta.gz")), SequenceFormat::Fasta);
/// ```
#[must_use]
pub fn from_extension(path: &Path) -> Self {
// Get the extension, stripping .gz if present
let ext = path
.extension()
.and_then(OsStr::to_str)
.map(str::to_lowercase);
let effective_ext = match ext.as_deref() {
Some("gz") => {
// Strip .gz and get the real extension
path.file_stem()
.and_then(|stem| Path::new(stem).extension())
.and_then(OsStr::to_str)
.map(str::to_lowercase)
}
other => other.map(String::from),
};
match effective_ext.as_deref() {
Some("fq" | "fastq") => Self::Fastq,
// Default to FASTA for known FASTA extensions and unknown extensions
_ => Self::Fasta,
}
}
/// Resolves `Auto` format to a concrete format based on the file path.
///
/// - If format is already `Fasta` or `Fastq`, returns it unchanged.
/// - If format is `Auto` and a path is provided, detects from extension.
/// - If format is `Auto` and no path is provided (stdin), defaults to `Fasta`.
///
/// # Examples
///
/// ```
/// use kmerust::format::SequenceFormat;
/// use std::path::Path;
///
/// // Auto-detection from path
/// let format = SequenceFormat::Auto.resolve(Some(Path::new("reads.fq")));
/// assert_eq!(format, SequenceFormat::Fastq);
///
/// // Explicit format is unchanged
/// let format = SequenceFormat::Fasta.resolve(Some(Path::new("reads.fq")));
/// assert_eq!(format, SequenceFormat::Fasta);
///
/// // Stdin defaults to FASTA
/// let format = SequenceFormat::Auto.resolve(None);
/// assert_eq!(format, SequenceFormat::Fasta);
/// ```
#[must_use]
pub fn resolve(self, path: Option<&Path>) -> Self {
match self {
Self::Auto => path.map_or(Self::Fasta, Self::from_extension),
other => other,
}
}
/// Returns `true` if this format is FASTQ.
#[must_use]
pub const fn is_fastq(self) -> bool {
matches!(self, Self::Fastq)
}
/// Returns `true` if this format is FASTA.
#[must_use]
pub const fn is_fasta(self) -> bool {
matches!(self, Self::Fasta)
}
}
impl std::fmt::Display for SequenceFormat {
fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
match self {
Self::Auto => write!(f, "auto"),
Self::Fasta => write!(f, "fasta"),
Self::Fastq => write!(f, "fastq"),
}
}
}
#[cfg(test)]
mod tests {
use super::*;
#[test]
fn from_extension_fasta() {
assert_eq!(
SequenceFormat::from_extension(Path::new("test.fa")),
SequenceFormat::Fasta
);
assert_eq!(
SequenceFormat::from_extension(Path::new("test.fasta")),
SequenceFormat::Fasta
);
assert_eq!(
SequenceFormat::from_extension(Path::new("test.fna")),
SequenceFormat::Fasta
);
}
#[test]
fn from_extension_fastq() {
assert_eq!(
SequenceFormat::from_extension(Path::new("test.fq")),
SequenceFormat::Fastq
);
assert_eq!(
SequenceFormat::from_extension(Path::new("test.fastq")),
SequenceFormat::Fastq
);
}
#[test]
fn from_extension_gzipped() {
assert_eq!(
SequenceFormat::from_extension(Path::new("test.fa.gz")),
SequenceFormat::Fasta
);
assert_eq!(
SequenceFormat::from_extension(Path::new("test.fasta.gz")),
SequenceFormat::Fasta
);
assert_eq!(
SequenceFormat::from_extension(Path::new("test.fq.gz")),
SequenceFormat::Fastq
);
assert_eq!(
SequenceFormat::from_extension(Path::new("test.fastq.gz")),
SequenceFormat::Fastq
);
}
#[test]
fn from_extension_unknown_defaults_to_fasta() {
assert_eq!(
SequenceFormat::from_extension(Path::new("test.txt")),
SequenceFormat::Fasta
);
assert_eq!(
SequenceFormat::from_extension(Path::new("test")),
SequenceFormat::Fasta
);
}
#[test]
fn resolve_auto_with_path() {
assert_eq!(
SequenceFormat::Auto.resolve(Some(Path::new("test.fq"))),
SequenceFormat::Fastq
);
assert_eq!(
SequenceFormat::Auto.resolve(Some(Path::new("test.fa"))),
SequenceFormat::Fasta
);
}
#[test]
fn resolve_auto_without_path() {
assert_eq!(SequenceFormat::Auto.resolve(None), SequenceFormat::Fasta);
}
#[test]
fn resolve_explicit_format_unchanged() {
assert_eq!(
SequenceFormat::Fasta.resolve(Some(Path::new("test.fq"))),
SequenceFormat::Fasta
);
assert_eq!(
SequenceFormat::Fastq.resolve(Some(Path::new("test.fa"))),
SequenceFormat::Fastq
);
}
#[test]
fn display() {
assert_eq!(format!("{}", SequenceFormat::Auto), "auto");
assert_eq!(format!("{}", SequenceFormat::Fasta), "fasta");
assert_eq!(format!("{}", SequenceFormat::Fastq), "fastq");
}
}