Struct InputBam 

pub struct InputBam {
    pub bam: String,
    pub filters: FiberFilters,
    pub global: GlobalOpts,
    pub header: Option<Header>,
}

This struct is used to parse the input bam file and the filters that should be applied to the bam file. This struct is parsed to create command line arguments and then passed to many functions.

Fields

bam: String

Input BAM file. If no path is provided stdin is used. For m6A prediction, this should be a HiFi bam file with kinetics data. For other commands, this should be a bam file with m6A calls.

filters: FiberFilters

global: GlobalOpts

header: Option<Header>

by skipping this field it is not parsed as a command line argument

Implementations

impl InputBam

pub fn bam_reader(&mut self) -> Reader

pub fn indexed_bam_reader(&mut self) -> IndexedReader

pub fn fibers<'a>(&self, bam: &'a mut Reader) -> FiberseqRecords<'a>

pub fn header_view(&self) -> HeaderView

pub fn header(&self) -> Header

pub fn bam_writer(&self, out: &str) -> Writer

pub fn add_pansn_prefix(&mut self, pansn_prefix: &str)

Add panSN-spec prefix to all contig names in the stored header This must be called after opening the BAM reader to have an effect

pub fn strip_pansn_spec(&mut self, delimiter: char)

Strip panSN-spec information from all contig names in the stored header using the provided delimiter character (e.g., ‘#’ for panSN format) This must be called after opening the BAM reader to have an effect

Trait Implementations

impl Args for InputBam

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 Debug for InputBam

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

Formats the value using the given formatter.

impl Default for InputBam

fn default() -> Self

Returns the “default value” for a type.

impl FromArgMatches for InputBam

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.