Struct FastQFile 

pub struct FastQFile {
    pub lowest_char: u8,
    /* private fields */
}

FASTQ file reader that supports plain text, gzip, and bzip2 compressed files.

Mirrors Sequence.FastQFile in Java. Uses a look-ahead design where readNext() is called at construction time and after each next() call, so hasNext() can report whether more sequences are available. In Rust we use Option<Sequence> stored in next_sequence for the same pattern.

Fields

lowest_char: u8

The lowest raw quality character seen so far (for Phred encoding detection).

Implementations

impl FastQFile

pub fn open<P: AsRef<Path>>(config: &FastQCConfig, path: P) -> Result<Self>

Open a FASTQ file for reading.

The Java constructor opens the file, wraps it in the appropriate decompression stream, and immediately calls readNext() to prime the look-ahead buffer.

Trait Implementations

impl SequenceFile for FastQFile

fn percent_complete(&self) -> f64

Java reads fis.getChannel().position() which gives the compressed byte position, then divides by file size (also compressed). For plain files this is exact; for compressed files it gives a rough estimate based on compressed bytes consumed.

For stdin, Java always returns 0 until EOF then 100. We replicate that.

fn next(&mut self) -> Option<Result<Sequence>>

Read the next sequence from the file, or None at EOF.

fn name(&self) -> &str

The display name of this file (typically the filename).

fn is_colorspace(&self) -> bool

Whether this file contains colorspace data (SOLiD).