Struct FilterOptions 

pub struct FilterOptions {
    pub list: Option<HashSet<Vec<u8>>>,
    pub list_file: Option<PathBuf>,
    pub bam: Option<PathBuf>,
    pub cram: Option<PathBuf>,
    pub fasta: Option<PathBuf>,
    pub fastq1: Option<PathBuf>,
    pub fastq2: Option<PathBuf>,
    pub suffix: String,
    pub fasta_out: bool,
    pub fastq_out: bool,
    pub read_list: Option<PathBuf>,
}

Options to pass to blobtk filter

Fields

list: Option<HashSet<Vec<u8>>>

List of sequence IDs

list_file: Option<PathBuf>

Path to input file containing a list of sequence IDs

bam: Option<PathBuf>

Path to BAM file

cram: Option<PathBuf>

Path to CRAM file

fasta: Option<PathBuf>

Path to assembly FASTA input file (required for CRAM)

fastq1: Option<PathBuf>

Path to FASTQ file to filter (forward or single reads)

fastq2: Option<PathBuf>

Path to paired FASTQ file to filter (reverse reads)

suffix: String

Suffix to use for output filtered files

fasta_out: bool

Flag to output a filtered FASTA file

fastq_out: bool

Flag to output filtered FASTQ files

read_list: Option<PathBuf>

Path to output list of read IDs

Trait Implementations

impl Args for FilterOptions

fn group_id() -> Option<Id>

Report the ArgGroup::id for this set of arguments

fn augment_args<'b>(__clap_app: Command) -> Command

Append to Command so it can instantiate Self via FromArgMatches::from_arg_matches_mut

fn augment_args_for_update<'b>(__clap_app: Command) -> Command

Append to Command so it can instantiate self via FromArgMatches::update_from_arg_matches_mut

impl CommandFactory for FilterOptions

fn command<'b>() -> Command

Build a Command that can instantiate Self.

fn command_for_update<'b>() -> Command

Build a Command that can update self.

impl Debug for FilterOptions

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl FromArgMatches for FilterOptions

fn from_arg_matches(__clap_arg_matches: &ArgMatches) -> Result<Self, Error>

Instantiate Self from ArgMatches, parsing the arguments as needed.

fn from_arg_matches_mut( __clap_arg_matches: &mut ArgMatches, ) -> Result<Self, Error>

Instantiate Self from ArgMatches, parsing the arguments as needed.

fn update_from_arg_matches( &mut self, __clap_arg_matches: &ArgMatches, ) -> Result<(), Error>

Assign values from ArgMatches to self.

fn update_from_arg_matches_mut( &mut self, __clap_arg_matches: &mut ArgMatches, ) -> Result<(), Error>

Assign values from ArgMatches to self.

impl Parser for FilterOptions

fn parse() -> Self

Parse from std::env::args_os(), exit on error.

fn try_parse() -> Result<Self, Error>

Parse from std::env::args_os(), return Err on error.

fn parse_from<I, T>(itr: I) -> Self

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Parse from iterator, exit on error.

fn try_parse_from<I, T>(itr: I) -> Result<Self, Error>

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Parse from iterator, return Err on error.

fn update_from<I, T>(&mut self, itr: I)

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Update from iterator, exit on error.

fn try_update_from<I, T>(&mut self, itr: I) -> Result<(), Error>

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Update from iterator, return Err on error.