Struct PileupOptions 

pub struct PileupOptions {

    pub input: InputBam,
    pub rgn: Vec<String>,
    pub bed: Option<String>,
    pub out: String,
    pub m6a: bool,
    pub cpg: bool,
    pub haps: bool,
    pub keep_zeros: bool,
    pub per_base: bool,
    pub fiber_coverage: bool,
    pub shuffle: Option<String>,
    pub rolling_max: Option<usize>,
    pub no_msp: bool,
    pub no_nuc: bool,
}

Fields

input: InputBam

rgn: Vec<String>

Region string(s) to make a pileup of. e.g. chr1:1-1000 or chr1:1-1,000 Can be specified multiple times for multiple regions. If not provided will make a pileup of the whole genome

bed: Option<String>

BED file with regions to query. If the BED file has a name column (4th column), the name will be added to each output line for that region.

out: String

Output file

m6a: bool

include m6A calls

cpg: bool

include 5mC calls

haps: bool

For each column add two new columns with the hap1 and hap2 specific data.

keep_zeros: bool

Keep zero coverage regions

per_base: bool

Write output one base at a time even if the values do not change

fiber_coverage: bool

Calculate coverage starting from the first MSP/NUC to the last MSP/NUC position instead of the complete span of the read alignment.

shuffle: Option<String>

Shuffle the fiber-seq data according to a bed file of the shuffled positions of the fiber-seq data

The bed file should have the following format: #chrom shuffled_start shuffled_end read_name original_start

rolling_max: Option<usize>

Output a rolling max of the score column over X bases

no_msp: bool

No MSP columns

no_nuc: bool

No NUC columns

Implementations

impl PileupOptions

pub fn effective_fiber_coverage(&self) -> bool

--fire-filter bundles --fiber-coverage in addition to the three filters. Callers should use this in place of reading fiber_coverage directly so the bundle stays coherent.

Trait Implementations

impl Args for PileupOptions

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 PileupOptions

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

Formats the value using the given formatter.

impl From<&PileupOptions> for FireTrackOptions

fn from(opts: &PileupOptions) -> Self

Converts to this type from the input type.

impl From<&PileupOptions> for FiberseqPileupOptions

fn from(opts: &PileupOptions) -> Self

Converts to this type from the input type.

impl FromArgMatches for PileupOptions

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.