Struct PileupPosition 

pub struct PileupPosition {

    pub ref_seq: String,
    pub pos: u32,
    pub ref_base: Option<char>,
    pub depth: u32,
    pub a: u32,
    pub c: u32,
    pub g: u32,
    pub t: u32,
    pub n: u32,
    pub r: u32,
    pub y: u32,
    pub s: u32,
    pub w: u32,
    pub k: u32,
    pub m: u32,
    pub ins: u32,
    pub del: u32,
    pub ref_skip: u32,
    pub fail: u32,
    pub count_of_mate_resolutions: u32,
    pub near_max_depth: bool,
}

Hold all information about a position.

Fields

ref_seq: String

Reference sequence name.

pos: u32

1-based position in the sequence.

ref_base: Option<char>

The reference base at this position.

depth: u32

Total depth at this position.

a: u32

Number of A bases at this position.

c: u32

Number of C bases at this position.

g: u32

Number of G bases at this position.

t: u32

Number of T bases at this position.

n: u32

Number of N bases at this position. Any unrecognized base will be counted as an N.

r: u32

Number of bases that could be A or G

y: u32

Number of bases that could be C or T

s: u32

Number of bases that could be G or C

w: u32

Number of bases that could be A or T

k: u32

Number of bases that could be G or T

m: u32

Number of bases that could be A or C

ins: u32

Number of insertions that start to the right of this position. Does not count toward depth.

del: u32

Number of deletions at this position.

ref_skip: u32

Number of refskips at this position. Does not count toward depth.

fail: u32

Number of reads failing filters at this position.

count_of_mate_resolutions: u32

Number of times a mate resolution was needed.

near_max_depth: bool

Depth is within 1% of max_depth

Implementations

impl PileupPosition

pub fn from_pileup<F: ReadFilter>( pileup: Pileup, header: &HeaderView, read_filter: &F, base_filter: Option<u8>, ) -> Self

Convert a pileup into a Position.

This will walk over each of the alignments and count the number each nucleotide it finds. It will also count the number of Ins/Dels/Skips that are at each position.

Arguments

• pileup - a pileup at a genomic position
• header - a headerview for the bam file being read, to get the sequence name
• read_filter - a function to filter out reads, returning false will cause a read to be filtered
• base_filter - an optional base quality score. If Some(number) if the base quality is not >= that number the base is treated as an N

pub fn from_pileup_mate_aware<F: ReadFilter>( pileup: Pileup, header: &HeaderView, read_filter: &F, base_filter: Option<u8>, mate_fix_strat: MateResolutionStrategy, ) -> Self

Convert a pileup into a Position.

This will walk over each of the alignments and count the number each nucleotide it finds. It will also count the number of Ins/Dels/Skips that are at each position.

Additionally, this method is mate aware. Before processing a position it will scan the alignments for mates. If a mate is found, it will try to take use the mate that has the highest MAPQ, breaking ties by choosing the first in pair that passes filters. In the event of both failing filters or not being first in pair, the first read encountered is kept.

Arguments

• pileup - a pileup at a genomic position
• header - a headerview for the bam file being read, to get the sequence name
• read_filter - a function to filter out reads, returning false will cause a read to be filtered
• base_filter - an optional base quality score. If Some(number) if the base quality is not >= that number the base is treated as an N

pub fn compact_refseq(header: &HeaderView, tid: u32) -> SmartString<LazyCompact>

Convert a tid to a SmartString<LazyCompact>.

Trait Implementations

impl Debug for PileupPosition

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

Formats the value using the given formatter.

impl Default for PileupPosition

fn default() -> PileupPosition

Returns the “default value” for a type.

impl Position for PileupPosition

fn new(ref_seq: String, pos: u32) -> Self

Create a new position for the given ref_seq name.

impl Serialize for PileupPosition

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error>

where __S: Serializer,

Serialize this value into the given Serde serializer.