Struct BAMFile 

pub struct BAMFile { /* private fields */ }

BAM/SAM file reader that supports both BAM and SAM input formats.

Mirrors Sequence.BAMFile in Java. Uses a look-ahead design where read_next() is called at construction time and after each next() call.

Implementations

impl BAMFile

pub fn open(path: &Path, is_bam: bool, only_mapped: bool) -> Result<Self>

Open a BAM or SAM file for reading.

If is_bam is true, the file is read as BAM format; otherwise as SAM. If only_mapped is true, unmapped reads are skipped.

The Java constructor opens the file, creates a SamReader with SILENT validation stringency, gets an iterator, and calls readNext() to prime the look-ahead buffer.

Trait Implementations

impl SequenceFile for BAMFile

fn is_colorspace(&self) -> bool

BAM/SAM files are never colorspace. Java’s BAMFile.isColorspace() always returns false.

fn percent_complete(&self) -> f64

Java tracks progress using the raw FileInputStream position divided by file size. For BAM files, this gives a rough estimate since the underlying file is BGZF compressed. We estimate using the record size heuristic from Java when precise position tracking is not available.

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).