Struct FilterConfig

pub struct FilterConfig {
    pub minimizers_path: PathBuf,
    pub input_path: String,
    pub input2_path: Option<String>,
    pub output_path: String,
    pub output2_path: Option<String>,
    pub match_threshold: MatchThreshold,
    pub prefix_length: usize,
    pub summary_path: Option<PathBuf>,
    pub deplete: bool,
    pub rename: bool,
    pub threads: usize,
}

Fields

minimizers_path: PathBuf

Minimizer index file path

input_path: String

Path to input fastx file (or - for stdin)

input2_path: Option<String>

Path to optional second paired fastx file (or - for interleaved stdin)

output_path: String

Path to output fastx file (or - for stdout; detects .gz and .zst)

output2_path: Option<String>

Path to optional second output fastx file for paired reads (detects .gz and .zst)

match_threshold: MatchThreshold

Match threshold for filtering sequences

prefix_length: usize

Consider only the first N nucleotides per sequence (0 = entire sequence)

summary_path: Option<PathBuf>

Path to JSON summary file

deplete: bool

Deplete mode (remove sequences WITH matches, original deacon behavior)

rename: bool

Replace sequence headers with sequential numbers (1, 2, 3…)

threads: usize

Number of execution threads (0 = auto)

Implementations

impl FilterConfig

pub fn new<P: AsRef<Path>>(minimizers_path: P) -> Self

pub fn with_input<S: Into<String>>(self, input_path: S) -> Self

pub fn with_input2<S: Into<String>>(self, input2_path: S) -> Self

pub fn with_output<S: Into<String>>(self, output_path: S) -> Self

pub fn with_output2<S: Into<String>>(self, output2_path: S) -> Self

pub fn with_match_threshold(self, match_threshold: MatchThreshold) -> Self

pub fn with_prefix_length(self, prefix_length: usize) -> Self

pub fn with_summary<P: AsRef<Path>>(self, summary_path: P) -> Self

pub fn with_deplete(self, deplete: bool) -> Self

pub fn with_rename(self, rename: bool) -> Self

pub fn with_threads(self, threads: usize) -> Self

pub fn execute(&self) -> Result<()>

Filter with this configuration