Struct Command 

pub struct Command {
    pub left_side: f64,
    pub right_side: f64,
    pub both_end: f64,
    pub in_bam: String,
    pub out_bam: String,
    pub inverse: bool,
    pub unalign: bool,
}

Remove alignments with high number of clipped base. Sometimes aligner has very loose scoring methods and write alignments with high abundant of soft/hard-clipped base into alignment BAM files. This program is for filtering these reads out by gating the number of clipped bases in relative to the read sequence length

Fields

left_side: f64

maximum fraction of bases on the sequence being clipped from the left side (5’ end)

right_side: f64

maximum fraction of bases on the sequence being clipped from the right side (3’ end)

both_end: f64

maximum fraction of total bases on the sequence being clipped

in_bam: String

input bam file path (“-” for stdin)

out_bam: String

output bam file path (“-” for stdout)

inverse: bool

keeping the failed ones (high-clipped-fraction alignments)

unalign: bool

make the record to unmapped instead of removing it, ignore –inverse flag

Trait Implementations

impl Args for Command

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

Append to Command so it can instantiate Self.

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

Append to Command so it can update self.

impl CommandFactory for Command

fn into_app<'b>() -> Command<'b>

Deprecated, replaced with CommandFactory::command

fn into_app_for_update<'b>() -> Command<'b>

Deprecated, replaced with CommandFactory::command_for_update

fn command<'help>() -> App<'help>

Build a Command that can instantiate Self.

fn command_for_update<'help>() -> App<'help>

Build a Command that can update self.

impl Debug for Command

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

Formats the value using the given formatter.

impl FromArgMatches for Command

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 Command

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.