Struct SamConfig 

pub struct SamConfig {

    pub print_as: bool,
    pub print_xs: bool,
    pub print_ys: bool,
    pub print_x0: bool,
    pub print_x1: bool,
    pub print_xn: bool,
    pub print_xm: bool,
    pub print_xo: bool,
    pub print_xg: bool,
    pub print_nm: bool,
    pub print_md: bool,
    pub print_yf: bool,
    pub print_yd: bool,
    pub print_yt: bool,
    pub print_zs: bool,
    pub print_nh: bool,
    pub print_hi: bool,
    pub print_nm_genome: bool,
    pub print_md_number: bool,
    pub print_jm: bool,
    pub print_ji: bool,
    pub full_ref: bool,
}

SAM output configuration

Fields

print_as: bool

Print AS:i: alignment score

print_xs: bool

Print XS:i: secondary alignment score

print_ys: bool

Print YS:i: mate alignment score

print_x0: bool

Print X0:i: number of best alignments

print_x1: bool

Print X1:i: number of suboptimal alignments

print_xn: bool

Print XN:i: number of Ns in reference

print_xm: bool

Print XM:i: number of mismatches

print_xo: bool

Print XO:i: number of gap opens

print_xg: bool

Print XG:i: number of gap extensions

print_nm: bool

Print NM:i: edit distance

print_md: bool

Print MD:Z: mismatch string

print_yf: bool

Print YF:Z: mate alignment flags

print_yd: bool

Print YD:i: mate distance

print_yt: bool

Print YT:Z: mate type

print_zs: bool

Print ZS:Z: strand

print_nh: bool

Print NH:i: hit count

print_hi: bool

Print HI:i: hit index

print_nm_genome: bool

Print nM:i: genome mismatches

print_md_number: bool

Print MD:n: mismatch as number

print_jm: bool

Print jM:i: junction mismatch

print_ji: bool

Print jI:i: junction insertions

full_ref: bool

Print full ref coords

Trait Implementations

impl Clone for SamConfig

fn clone(&self) -> SamConfig

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for SamConfig

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

Formats the value using the given formatter.

impl Default for SamConfig

fn default() -> Self

Returns the “default value” for a type.