Struct Eval 

pub struct Eval {
    pub mapped: PathBuf,
    pub truth: Option<PathBuf>,
    pub output: OutputPrefixOptions,
    pub wiggle: u32,
}

Evaluate alignment accuracy of simulated reads.

Compares the true (simulated) positions of reads against their mapped positions in a BAM file. Reports mapping accuracy, mismapping rate, and unmapped rate stratified by MAPQ bin. Truth positions are parsed from encoded read names (default holodeck format).

Fields

mapped: PathBuf

BAM file of mapped reads to evaluate.

truth: Option<PathBuf>

Optional golden BAM file with truth alignments. If omitted, truth positions are parsed from encoded read names.

output: OutputPrefixOptions

wiggle: u32

Maximum distance (in bases) between the true and mapped start positions of a read for it to be considered correctly mapped. Uses |mapped_start - true_start| <= wiggle on the same contig.

Trait Implementations

impl Args for Eval

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 Command for Eval

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

Execute the command.

impl CommandFactory for Eval

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 Eval

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

Formats the value using the given formatter.

impl FromArgMatches for Eval

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 Eval

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.