Struct PerSequenceGCContent 

pub struct PerSequenceGCContent { /* private fields */ }

Implementations

impl PerSequenceGCContent

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

Trait Implementations

impl QCModule for PerSequenceGCContent

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

Process a single sequence record, accumulating statistics.

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 finalize(&mut self)

Finalize calculations after all sequences have been processed.

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 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 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 status(&self) -> ModuleStatus

The current status of this module.

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

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