Struct RegionSet

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pub struct RegionSet {
    pub regions: Vec<Region>,
    pub header: Option<String>,
    pub path: Option<PathBuf>,
}

Expand description

RegionSet struct, the representation of the interval region set file, such as bed file.

Fields§

§regions: Vec<Region>§header: Option<String>§path: Option<PathBuf>

Implementations§

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impl RegionSet

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pub fn to_bed<T: AsRef<Path>>(&self, path: T) -> Result<()>

Save a regionset to disk as bed file

§Arguments

path: the path to the file to dump to

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pub fn to_bed_gz<T: AsRef<Path>>(&self, path: T) -> Result<()>

Save a regionset to disk as bed.gz file

§Arguments

path: the path to the file to dump to

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pub fn identifier(&self) -> String

Calculate identifier for RegionSet

This function doesn’t sort file, and identifer is based on unsorted first 3 columns.

§Returns

String containing RegionSet identifier

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pub fn file_digest(&self) -> String

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pub fn iter_chroms(&self) -> impl Iterator<Item = &String>

Iterate unique chromosomes located in RegionSet

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pub fn iter_chr_regions<'a>( &'a self, chr: &'a str, ) -> impl Iterator<Item = &'a Region>

Iterate through regions located on specific Chromosome in RegionSet

§Arguments

chr: chromosome name

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pub fn sort(&mut self)

Sort bed file based on first 3 columns. Sorting is happening inside the object, where original order will be overwritten

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pub fn is_empty(&self) -> bool

Is regionSet empty?

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pub fn region_widths(&self) -> Vec<u32>

Calculate all regions width

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pub fn mean_region_width(&self) -> f64

Calculate mean region width for whole RegionSet

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pub fn calc_mid_points(&self) -> HashMap<String, Vec<u32>>

Calculate middle point for each region, and return hashmap with midpoints for each chromosome

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pub fn calc_mid_points_with_mode( &self, mode: CoordinateMode, ) -> HashMap<String, Vec<u32>>

Calculate midpoints using the specified coordinate convention.

See Region::mid_point_with_mode for details on how each mode computes the midpoint.

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pub fn len(&self) -> usize

Get number of regions in RegionSet

Returns: number of regions

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pub fn get_max_end_per_chr(&self) -> HashMap<String, u32>

Get the furthest region location for each region

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pub fn nucleotides_length(&self) -> u32

Get total nucleotide count

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impl RegionSet

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pub fn reduce(&self) -> RegionSet

Merge overlapping and adjacent intervals per chromosome.

Sorts by (chr, start), then sweeps to merge intervals where next.start <= current.end. Returns a minimal set of non-overlapping regions.

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pub fn concat(&self, other: &RegionSet) -> RegionSet

Combine two region sets without merging overlapping intervals.

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pub fn concat_into(self, other: RegionSet) -> RegionSet

Combine two region sets without merging overlapping intervals, consuming both sets.

Like RegionSet::concat, but takes ownership of self and other so the backing Vec<Region>s are moved instead of cloned. Prefer this when neither input is needed afterward. As with concat, the resulting set has no header or path (it is a pure-regions set).

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pub fn union(&self, other: &RegionSet) -> RegionSet

Merge two region sets into a minimal non-overlapping set.

Equivalent to self.concat(other).reduce().

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pub fn union_into(self, other: RegionSet) -> RegionSet

Merge two region sets into a minimal non-overlapping set, consuming both.

Equivalent to self.concat_into(other).reduce(). Saves the concat-stage clones that RegionSet::union incurs; reduce still allocates internally.

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pub fn trim(&self, chrom_sizes: &HashMap<String, u32>) -> RegionSet

Clamp regions to chromosome boundaries.

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pub fn gaps(&self, chrom_sizes: &HashMap<String, u32>) -> RegionSet

Return the gaps between regions per chromosome, bounded by chromosome sizes.

Reduces the input first, then emits intervals that tile the peak-free regions of each chromosome listed in chrom_sizes:

a leading gap from position 0 to the first region’s start (omitted if the first region starts at 0),
an inter-region gap between each consecutive pair of reduced regions,
a trailing gap from the last region’s end to the chromosome size (omitted if the last region already reaches the chromosome end, or extends past it due to assembly mismatch),
a full-chromosome gap 0..chrom_size for any chromosome in chrom_sizes that has no regions at all.

Regions on chromosomes not present in chrom_sizes are skipped. Regions that extend past the stated chromosome size are clipped to chrom_size when computing the trailing gap, matching the clipping behavior of trim().

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pub fn shift(&self, offset: i64) -> RegionSet

Shift all regions by a fixed offset.

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pub fn flank(&self, width: u32, use_start: bool, both: bool) -> RegionSet

Generate flanking regions.

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pub fn resize(&self, width: u32, fix: &str) -> RegionSet

Resize regions to a fixed width, anchored at start, end, or center.

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pub fn narrow( &self, start: Option<u32>, end: Option<u32>, width: Option<u32>, ) -> RegionSet

Narrow each region by specifying a relative sub-range within it.

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pub fn promoters(&self, upstream: u32, downstream: u32) -> RegionSet

Generate promoter regions relative to each region’s start position.

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pub fn pintersect(&self, other: &RegionSet) -> RegionSet

Pairwise intersection of two region sets by index position.

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pub fn disjoin(&self) -> RegionSet

Break all regions into non-overlapping disjoint pieces.

Internal boundaries (starts and ends of overlapping input regions) split the covered intervals into non-overlapping pieces. Only pieces that are covered by at least one input region are emitted; gaps between disjoint regions are never filled. This matches the semantics of R’s GenomicRanges disjoin.

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