Struct BasicStats 

pub struct BasicStats { /* private fields */ }

Implementations

impl BasicStats

pub fn new(_limits: &Limits) -> Self

pub fn set_file_name(&mut self, name: &str)

Set the filename, stripping any “stdin:” prefix.

Matches setFileName() which strips “stdin:” prefix.

Trait Implementations

impl QCModule for BasicStats

fn finalize(&mut self)

Publish the final counters so the progress table ends on exactly the values that go into the report.

fn cost_hint(&self) -> u32

A rough, static hint of this module’s per-sequence processing cost relative to the other modules. It is used only to balance the modules across worker threads in the parallel analysis pipeline, so that the few expensive modules don’t pile onto one thread. The values are approximate and never affect results — a wrong hint only costs a little parallel efficiency, never correctness. Keep them in proportion to a profile of the default modules on short reads; the default suits a near-free module.

fn process_sequence(&mut self, sequence: &Sequence)

Process a single sequence record, accumulating statistics.

fn attach_live_stats(&mut self, live: Arc<LiveStats>)

Attach a shared snapshot sink that the module publishes partial results to while it runs, so the terminal progress display can show live statistics. Only BasicStats implements this; every other module ignores it, and nothing about the analysis changes when no sink is attached.

fn set_filename(&mut self, name: &str)

Set the source filename for this module. BasicStats uses this to display the filename in the report. Other modules ignore it.

fn set_phred_encoding(&mut self, encoding: PhredEncoding)

Tell the module the quality encoding specified by the input format, when there is one (BAM/SAM, where quality is Phred+33 by construction). Modules that would otherwise infer the encoding from the lowest quality character use this instead; other modules ignore it. Never called for formats like FASTQ where the encoding must be inferred.

fn name(&self) -> &str

The display name of this module as shown in the report.

fn description(&self) -> &str

A longer description of what this module checks.

fn reset(&mut self)

Reset the module to its initial state.

fn raises_error(&self) -> bool

Whether the module results should trigger a failure status.

fn raises_warning(&self) -> bool

Whether the module results should trigger a warning status.

fn ignore_filtered_sequences(&self) -> bool

Whether this module should skip sequences flagged as filtered.

fn ignore_in_report(&self) -> bool

Whether this module should be excluded from the report. Matches ignoreInReport() - used e.g. by PerTileQuality when there are no tile IDs in the data.

fn write_text_report(&self, writer: &mut dyn Write) -> Result<()>

Write this module’s section to the text report.

fn status(&self) -> ModuleStatus

The current status of this module.

fn chart_image_name(&self) -> Option<&str>

Return the base filename for this module’s chart image (without extension). Matches the filenames used in Images/ directory of the zip archive, e.g. “per_base_quality” for per_base_quality.png and per_base_quality.svg.

fn chart_alt_text(&self) -> Option<&str>

Return the alt text for this module’s chart image, if it has one. Modules that produce charts should override this to return Some(“…”). The default write_html_report uses this to call write_chart_and_table automatically, so modules with charts only need to implement this method instead of overriding write_html_report.

fn generate_chart_svg(&self) -> Option<String>

Generate the SVG chart content for this module, if applicable. In Java, writeDefaultImage() renders the Swing JPanel to both SVG and PNG. Here we generate SVG first, then convert to PNG via resvg.

fn write_html_report(&self, writer: &mut dyn Write, png: bool) -> Result<()>

Write this module’s HTML content (table and/or chart image) to the report.